Mercurial > repos > bgruening > jbrowse2

annotate jbrowse2.py @ 0:53c2be00bb6f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
author bgruening
date Wed, 05 Jun 2024 08:15:49 +0000
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53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1 #!/usr/bin/env python
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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2
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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3 import argparse
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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4 import binascii
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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5 import datetime
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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6 # import hashlib
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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7 import json
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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8 import logging
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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9 import os
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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10 import re
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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11 import shutil
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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12 import ssl
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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13 import struct
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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14 import subprocess
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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15 import tempfile
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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16 import urllib.request
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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17 import xml.etree.ElementTree as ET
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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18 from collections import defaultdict
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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19
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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20 logging.basicConfig(level=logging.DEBUG)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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21 log = logging.getLogger("jbrowse")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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23 JB2VER = "v2.11.0"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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24 # version pinned if cloning - but not used until now
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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25 logCommands = True
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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26 # useful for seeing what's being written but not for production setups
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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27 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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28 SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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29 GALAXY_INFRASTRUCTURE_URL = None
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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30 mapped_chars = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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31 ">": "__gt__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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32 "<": "__lt__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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33 "'": "__sq__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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34 '"': "__dq__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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35 "[": "__ob__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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36 "]": "__cb__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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37 "{": "__oc__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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38 "}": "__cc__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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39 "@": "__at__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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40 "#": "__pd__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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41 "": "__cn__",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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42 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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43
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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44
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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45 INDEX_TEMPLATE = """<!doctype html>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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46 <html lang="en" style="height:100%">
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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47 <head>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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48 <meta charset="utf-8"/>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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49 <link rel="shortcut icon" href="./favicon.ico"/>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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50 <meta name="viewport" content="width=device-width,initial-scale=1"/>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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51 <meta name="theme-color" content="#000000"/>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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52 <meta name="description" content="A fast and flexible genome browser"/>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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53 <link rel="manifest" href="./manifest.json"/>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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54 <title>JBrowse</title>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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55 </script>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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56 </head>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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57 <body style="overscroll-behavior:none; height:100%; margin: 0;">
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58 <iframe
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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59 id="jbframe"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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60 title="JBrowse2"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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61 frameborder="0"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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62 width="100%"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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63 height="100%"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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64 src='index_noview.html?config=config.json__SESSION_SPEC__'>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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65 </iframe>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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66 </body>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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67 </html>
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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68 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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69
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70
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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71 class ColorScaling(object):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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72
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73 COLOR_FUNCTION_TEMPLATE = """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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74 function(feature, variableName, glyphObject, track) {{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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75 var score = {score};
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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76 {opacity}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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77 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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78 }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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79 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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80
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81 COLOR_FUNCTION_TEMPLATE_QUAL = r"""
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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82 function(feature, variableName, glyphObject, track) {{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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83 var search_up = function self(sf, attr){{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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84 if(sf.get(attr) !== undefined){{
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85 return sf.get(attr);
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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86 }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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87 if(sf.parent() === undefined) {{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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88 return;
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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89 }}else{{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
90 return self(sf.parent(), attr);
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
91 }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
92 }};
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
93
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
94 var search_down = function self(sf, attr){{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
95 if(sf.get(attr) !== undefined){{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
96 return sf.get(attr);
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
97 }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
98 if(sf.children() === undefined) {{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
99 return;
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
100 }}else{{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
101 var kids = sf.children();
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
102 for(var child_idx in kids){{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
103 var x = self(kids[child_idx], attr);
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
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diff changeset
104 if(x !== undefined){{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
105 return x;
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
106 }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
107 }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
108 return;
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
109 }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
110 }};
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
111
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
112 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color});
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
113 var score = (search_up(feature, 'score') || search_down(feature, 'score'));
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
114 {opacity}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
115 if(score === undefined){{ opacity = 1; }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
116 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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117 var red = parseInt(result[1], 16);
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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118 var green = parseInt(result[2], 16);
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
119 var blue = parseInt(result[3], 16);
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
120 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
121 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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122 }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
123 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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124
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
125 OPACITY_MATH = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
126 "linear": """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
127 var opacity = (score - ({min})) / (({max}) - ({min}));
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
128 """,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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129 "logarithmic": """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
130 var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min}));
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
131 """,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
132 "blast": """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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133 var opacity = 0;
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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134 if(score == 0.0) {{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
135 opacity = 1;
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
136 }} else {{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
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diff changeset
137 opacity = (20 - Math.log10(score)) / 180;
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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138 }}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
139 """,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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140 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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141
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
142 BREWER_COLOUR_IDX = 0
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
143 BREWER_COLOUR_SCHEMES = [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
144 (166, 206, 227),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
145 (31, 120, 180),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
146 (178, 223, 138),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
147 (51, 160, 44),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
148 (251, 154, 153),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
149 (227, 26, 28),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
150 (253, 191, 111),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
151 (255, 127, 0),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
152 (202, 178, 214),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
153 (106, 61, 154),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
154 (255, 255, 153),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
155 (177, 89, 40),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
156 (228, 26, 28),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
157 (55, 126, 184),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
158 (77, 175, 74),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
159 (152, 78, 163),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
160 (255, 127, 0),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
161 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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162
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
163 BREWER_DIVERGING_PALLETES = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
164 "BrBg": ("#543005", "#003c30"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
165 "PiYg": ("#8e0152", "#276419"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
166 "PRGn": ("#40004b", "#00441b"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
167 "PuOr": ("#7f3b08", "#2d004b"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
168 "RdBu": ("#67001f", "#053061"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
169 "RdGy": ("#67001f", "#1a1a1a"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
170 "RdYlBu": ("#a50026", "#313695"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
171 "RdYlGn": ("#a50026", "#006837"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
172 "Spectral": ("#9e0142", "#5e4fa2"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
173 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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174
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
175 def __init__(self):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
176 self.brewer_colour_idx = 0
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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177
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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178 def rgb_from_hex(self, hexstr):
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179 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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180 return struct.unpack("BBB", binascii.unhexlify(hexstr))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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181
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182 def min_max_gff(self, gff_file):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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183 min_val = None
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184 max_val = None
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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185 with open(gff_file, "r") as handle:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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186 for line in handle:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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187 try:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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188 value = float(line.split("\t")[5])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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189 min_val = min(value, (min_val or value))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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190 max_val = max(value, (max_val or value))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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191
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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192 if value < min_val:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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193 min_val = value
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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194
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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195 if value > max_val:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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196 max_val = value
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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197 except Exception:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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198 pass
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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199 return min_val, max_val
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200
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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201 def hex_from_rgb(self, r, g, b):
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202 return "#%02x%02x%02x" % (r, g, b)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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203
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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204 def _get_colours(self):
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205 r, g, b = self.BREWER_COLOUR_SCHEMES[
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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206 self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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207 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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208 self.brewer_colour_idx += 1
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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209 return r, g, b
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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210
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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211 def parse_menus(self, track):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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212 trackConfig = {"menuTemplate": [{}, {}, {}, {}]}
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213
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214 if "menu" in track["menus"]:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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215 menu_list = [track["menus"]["menu"]]
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216 if isinstance(track["menus"]["menu"], list):
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217 menu_list = track["menus"]["menu"]
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218
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219 for m in menu_list:
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220 tpl = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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221 "action": m["action"],
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222 "label": m.get("label", "{name}"),
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223 "iconClass": m.get("iconClass", "dijitIconBookmark"),
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224 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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225 if "url" in m:
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226 tpl["url"] = m["url"]
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227 if "content" in m:
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228 tpl["content"] = m["content"]
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229 if "title" in m:
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230 tpl["title"] = m["title"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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231
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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232 trackConfig["menuTemplate"].append(tpl)
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233
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234 return trackConfig
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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235
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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236 def parse_colours(self, track, trackFormat, gff3=None):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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237 # Wiggle tracks have a bicolor pallete
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238 trackConfig = {"style": {}}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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239 if trackFormat == "wiggle":
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240
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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241 trackConfig["style"]["pos_color"] = track["wiggle"]["color_pos"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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242 trackConfig["style"]["neg_color"] = track["wiggle"]["color_neg"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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243
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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244 if trackConfig["style"]["pos_color"] == "__auto__":
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245 trackConfig["style"]["neg_color"] = self.hex_from_rgb(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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246 *self._get_colours()
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247 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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248 trackConfig["style"]["pos_color"] = self.hex_from_rgb(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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249 *self._get_colours()
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250 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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251
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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252 # Wiggle tracks can change colour at a specified place
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253 bc_pivot = track["wiggle"]["bicolor_pivot"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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254 if bc_pivot not in ("mean", "zero"):
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255 # The values are either one of those two strings
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256 # or a number
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257 bc_pivot = float(bc_pivot)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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258 trackConfig["bicolor_pivot"] = bc_pivot
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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259 elif "scaling" in track:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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260 if track["scaling"]["method"] == "ignore":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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261 if track["scaling"]["scheme"]["color"] != "__auto__":
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262 trackConfig["style"]["color"] = track["scaling"]["scheme"]["color"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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263 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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264 trackConfig["style"]["color"] = self.hex_from_rgb(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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265 *self._get_colours()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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266 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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267 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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268 # Scored method
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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269 algo = track["scaling"]["algo"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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270 # linear, logarithmic, blast
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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271 scales = track["scaling"]["scales"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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272 # type __auto__, manual (min, max)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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273 scheme = track["scaling"]["scheme"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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274 # scheme -> (type (opacity), color)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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275 # ==================================
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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276 # GENE CALLS OR BLAST
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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277 # ==================================
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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278 if trackFormat == "blast":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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279 red, green, blue = self._get_colours()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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280 color_function = self.COLOR_FUNCTION_TEMPLATE.format(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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281 **{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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282 "score": "feature._parent.get('score')",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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283 "opacity": self.OPACITY_MATH["blast"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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284 "red": red,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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285 "green": green,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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286 "blue": blue,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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287 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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288 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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289 trackConfig["style"]["color"] = color_function.replace("\n", "")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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290 elif trackFormat == "gene_calls":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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291 # Default values, based on GFF3 spec
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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292 min_val = 0
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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293 max_val = 1000
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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294 # Get min/max and build a scoring function since JBrowse doesn't
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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295 if scales["type"] == "automatic" or scales["type"] == "__auto__":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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296 min_val, max_val = self.min_max_gff(gff3)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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297 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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298 min_val = scales.get("min", 0)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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299 max_val = scales.get("max", 1000)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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300
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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301 if scheme["color"] == "__auto__":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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302 user_color = "undefined"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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303 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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304 elif scheme["color"].startswith("#"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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305 user_color = "'%s'" % self.hex_from_rgb(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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306 *self.rgb_from_hex(scheme["color"][1:])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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307 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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308 auto_color = "undefined"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
309 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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310 user_color = "undefined"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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311 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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312
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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313 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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314 **{
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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315 "opacity": self.OPACITY_MATH[algo].format(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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316 **{"max": max_val, "min": min_val}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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317 ),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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318 "user_spec_color": user_color,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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319 "auto_gen_color": auto_color,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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320 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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321 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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322
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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323 trackConfig["style"]["color"] = color_function.replace("\n", "")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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324 return trackConfig
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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325
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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326
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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327 def etree_to_dict(t):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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328 if t is None:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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329 return {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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330
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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331 d = {t.tag: {} if t.attrib else None}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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332 children = list(t)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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333 if children:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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334 dd = defaultdict(list)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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335 for dc in map(etree_to_dict, children):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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336 for k, v in dc.items():
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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337 dd[k].append(v)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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338 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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339 if t.attrib:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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340 d[t.tag].update(("@" + k, v) for k, v in t.attrib.items())
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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341 if t.text:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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342 text = t.text.strip()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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343 if children or t.attrib:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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344 if text:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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345 d[t.tag]["#text"] = text
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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346 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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347 d[t.tag] = text
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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348 return d
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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349
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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350
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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351 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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352
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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353
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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354 def metadata_from_node(node):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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355 metadata = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
356 try:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
357 if len(node.findall("dataset")) != 1:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
358 # exit early
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
359 return metadata
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
360 except Exception:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
361 return {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
362
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
363 for (key, value) in node.findall("dataset")[0].attrib.items():
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
364 metadata["dataset_%s" % key] = value
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
365
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
366 if node.findall("history"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
367 for (key, value) in node.findall("history")[0].attrib.items():
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
368 metadata["history_%s" % key] = value
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
369
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
370 if node.findall("metadata"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
371 for (key, value) in node.findall("metadata")[0].attrib.items():
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
372 metadata["metadata_%s" % key] = value
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
373 # Additional Mappings applied:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
374 metadata[
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
375 "dataset_edam_format"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
376 ] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
377 metadata["dataset_edam_format"], metadata["dataset_file_ext"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
378 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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379 metadata["history_user_email"] = '<a href="mailto:{0}">{0}</a>'.format(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
380 metadata["history_user_email"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
381 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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382 metadata["hist_name"] = metadata["history_display_name"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
383 metadata[
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
384 "history_display_name"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
385 ] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
386 galaxy=GALAXY_INFRASTRUCTURE_URL,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
387 encoded_hist_id=metadata.get("history_id", "not available"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
388 hist_name=metadata.get("history_display_name", "not available"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
389 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
390 if node.findall("tool"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
391 for (key, value) in node.findall("tool")[0].attrib.items():
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
392 metadata["tool_%s" % key] = value
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
393 metadata[
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
394 "tool_tool"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
395 ] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}{tool_version}</a>'.format(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
396 galaxy=GALAXY_INFRASTRUCTURE_URL,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
397 encoded_id=metadata.get("dataset_id", ""),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
398 tool_id=metadata.get("tool_tool_id", ""),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
399 tool_version=metadata.get("tool_tool_version", ""),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
400 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
401 return metadata
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
402
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
403
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
404 class JbrowseConnector(object):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
405 def __init__(self, outdir, jbrowse2path):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
406 self.trackCounter = 0 # to avoid name clashes
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
407 self.assemblies = [] # these require more than a few line diff.
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
408 self.assmeta = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
409 self.ass_first_contigs = (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
410 []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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411 ) # for default session - these are read as first line of the assembly .fai
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
412 self.giURL = GALAXY_INFRASTRUCTURE_URL
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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413 self.outdir = outdir
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
414 self.jbrowse2path = jbrowse2path
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
415 os.makedirs(self.outdir, exist_ok=True)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
416 self.genome_names = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
417 self.trackIdlist = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
418 self.tracksToAdd = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
419 self.config_json = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
420 self.config_json_file = os.path.join(outdir, "config.json")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
421 self.clone_jbrowse()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
422
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
423 def get_cwd(self, cwd):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
424 if cwd:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
425 return self.outdir
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
426 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
427 return subprocess.check_output(["pwd"]).decode("utf-8").strip()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
428
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
429 def subprocess_check_call(self, command, output=None, cwd=True):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
430 if output:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
431 if logCommands:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
432 log.debug(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
433 "cd %s && %s > %s", self.get_cwd(cwd), " ".join(command), output
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
434 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
435 subprocess.check_call(command, cwd=self.get_cwd(cwd), stdout=output)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
436 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
437 if logCommands:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
438 log.debug("cd %s && %s", self.get_cwd(cwd), " ".join(command))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
439 subprocess.check_call(command, cwd=self.get_cwd(cwd))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
440
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
441 def subprocess_popen(self, command, cwd=True):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
442 if logCommands:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
443 log.debug(command)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
444 p = subprocess.Popen(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
445 command,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
446 cwd=self.get_cwd(cwd),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
447 shell=True,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
448 stdin=subprocess.PIPE,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
449 stdout=subprocess.PIPE,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
450 stderr=subprocess.PIPE,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
451 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
452 output, err = p.communicate()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
453 retcode = p.returncode
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
454 if retcode != 0:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
455 log.error(command)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
456 log.error(output)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
457 log.error(err)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
458 raise RuntimeError(f"Command ( {command} ) failed with exit code {retcode}")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
459
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
460 def subprocess_check_output(self, command):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
461 if logCommands:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
462 log.debug(" ".join(command))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
463 return subprocess.check_output(command, cwd=self.outdir)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
464
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
465 def symlink_or_copy(self, src, dest):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
466 if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
467 os.environ["GALAXY_JBROWSE_SYMLINKS"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
468 ):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
469 cmd = ["ln", "-s", src, dest]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
470 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
471 cmd = ["cp", src, dest]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
472
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
473 return self.subprocess_check_call(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
474
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
475 def _prepare_track_style(self, trackDict):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
476
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
477 style_data = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
478 "type": "LinearBasicDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
479 "displayId": "%s-LinearBasicDisplay" % trackDict["trackId"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
480 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
481
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
482 if trackDict.get("displays", None): # use first if multiple like bed
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
483 style_data["type"] = trackDict["displays"][0]["type"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
484 style_data["displayId"] = trackDict["displays"][0]["displayId"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
485 return style_data
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
486
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
487 def getNrow(self, url):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
488 useuri = url.startswith("https://") or url.startswith("http://")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
489 if not useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
490 fl = open(url, "r").readlines()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
491 nrow = len(fl)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
492 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
493 try:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
494 scontext = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
495 scontext.check_hostname = False
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
496 scontext.verify_mode = ssl.VerifyMode.CERT_NONE
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
497 with urllib.request.urlopen(url, context=scontext) as f:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
498 fl = f.readlines()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
499 nrow = len(fl)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
500 except Exception:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
501 nrow = 0
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
502 logging.debug("getNrow %s returning %d" % (url, nrow))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
503 return nrow
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
504
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
505 def process_genomes(self, genomes):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
506 assembly = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
507 assmeta = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
508 useuri = False
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
509 primaryGenome = None
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
510 for i, genome_node in enumerate(genomes):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
511 this_genome = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
512 if genome_node["useuri"] == "yes":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
513 useuri = True
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
514 genome_name = genome_node["label"].strip()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
515 if len(genome_name) == 0:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
516 genome_name = os.path.splitext(os.path.basename(genome_node["path"]))[0]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
517 if len(genome_name.split()) > 1:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
518 genome_name = genome_name.split()[0]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
519 # spaces and cruft break scripts when substituted
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
520 if not primaryGenome:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
521 primaryGenome = genome_name
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
522 if genome_name not in self.genome_names:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
523 self.genome_names.append(genome_name)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
524 fapath = genome_node["path"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
525 if not useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
526 fapath = os.path.realpath(fapath)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
527 assem, first_contig = self.make_assembly(fapath, genome_name, useuri)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
528 assembly.append(assem)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
529 self.ass_first_contigs.append(first_contig)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
530 if genome_name == primaryGenome: # first one
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
531 this_genome["genome_name"] = genome_name # first one for all tracks
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
532 this_genome["genome_sequence_adapter"] = assem["sequence"][
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
533 "adapter"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
534 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
535 this_genome["genome_firstcontig"] = first_contig
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
536 assmeta.append(this_genome)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
537 self.assemblies += assembly
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
538 self.assmeta[primaryGenome] = assmeta
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
539 self.tracksToAdd[primaryGenome] = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
540 return primaryGenome
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
541
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
542 def make_assembly(self, fapath, gname, useuri):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
543 if useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
544 faname = fapath
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
545 scontext = ssl.SSLContext(ssl.PROTOCOL_TLS_CLIENT)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
546 scontext.check_hostname = False
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
547 scontext.verify_mode = ssl.VerifyMode.CERT_NONE
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
548 with urllib.request.urlopen(url=faname + ".fai", context=scontext) as f:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
549 fl = f.readline()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
550 contig = fl.decode("utf8").strip()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
551 # Merlin 172788 8 60 61
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
552 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
553 faname = gname + ".fa.gz"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
554 fadest = os.path.realpath(os.path.join(self.outdir, faname))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
555 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
556 fapath,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
557 fadest,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
558 fadest,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
559 fadest,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
560 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
561 self.subprocess_popen(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
562 contig = open(fadest + ".fai", "r").readline().strip()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
563 adapter = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
564 "type": "BgzipFastaAdapter",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
565 "fastaLocation": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
566 "uri": faname,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
567 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
568 "faiLocation": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
569 "uri": faname + ".fai",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
570 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
571 "gziLocation": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
572 "uri": faname + ".gzi",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
573 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
574 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
575 first_contig = contig.split()[:2]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
576 first_contig.insert(0, gname)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
577 trackDict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
578 "name": gname,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
579 "sequence": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
580 "type": "ReferenceSequenceTrack",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
581 "trackId": gname,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
582 "adapter": adapter,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
583 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
584 "displays": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
585 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
586 "type": "LinearReferenceSequenceDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
587 "displayId": "%s-LinearReferenceSequenceDisplay" % gname,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
588 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
589 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
590 "type": "LinearGCContentDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
591 "displayId": "%s-LinearGCContentDisplay" % gname,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
592 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
593 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
594 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
595 return (trackDict, first_contig)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
596
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
597 def add_default_view(self):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
598 cmd = [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
599 "jbrowse",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
600 "set-default-session",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
601 "-s",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
602 self.config_json_file,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
603 "-t",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
604 ",".join(self.trackIdlist),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
605 "-n",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
606 "JBrowse2 in Galaxy",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
607 "--target",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
608 self.config_json_file,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
609 "-v",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
610 " LinearGenomeView",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
611 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
612 self.subprocess_check_call(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
613
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
614 def write_config(self):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
615 with open(self.config_json_file, "w") as fp:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
616 json.dump(self.config_json, fp, indent=2)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
617
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
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diff changeset
618 def text_index(self):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
619 # Index tracks
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
620 args = [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
621 "jbrowse",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
622 "text-index",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
623 "--target",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
624 self.outdir,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
625 "--assemblies",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
626 self.genome_name,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
627 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
628
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
629 tracks = ",".join(self.trackIdlist)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
630 if tracks:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
631 args += ["--tracks", tracks]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
632
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
633 self.subprocess_check_call(args)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
634
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
635 def add_hic(self, data, trackData):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
636 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
637 HiC adapter.
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
638 https://github.com/aidenlab/hic-format/blob/master/HiCFormatV9.md
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
639 for testing locally, these work:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
640 HiC data is from https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
641 using hg19 reference track as a
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
642 'BgzipFastaAdapter'
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
643 fastaLocation:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
644 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz',
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
645 faiLocation:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
646 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai',
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
647 gziLocation:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
648 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi',
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
649 Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
650
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
651 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
652 tId = trackData["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
653 wasCool = trackData["wasCool"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
654 # can be served - if public.
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
655 # dsId = trackData["metadata"]["dataset_id"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
656 # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
657 useuri = trackData["useuri"].lower() == "yes"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
658 logging.debug("wasCool=%s, data=%s, tId=%s" % (wasCool, data, tId))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
659 if useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
660 uri = data
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
661 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
662 uri = tId + ".hic"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
663 if not wasCool:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
664 dest = os.path.join(self.outdir, uri)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
665 if not os.path.exists(dest):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
666 cmd = ["cp", data, dest]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
667 self.subprocess_check_call(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
668 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
669 logging.error("not wasCool but %s exists" % dest)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
670 categ = trackData["category"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
671 trackDict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
672 "type": "HicTrack",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
673 "trackId": tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
674 "name": trackData["name"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
675 "assemblyNames": [trackData["assemblyNames"]],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
676 "category": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
677 categ,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
678 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
679 "adapter": {"type": "HicAdapter", "hicLocation": {"uri": uri}},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
680 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
681 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
682 self.trackIdlist.append(tId)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
683
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
684 def add_maf(self, data, trackData):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
685 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
686 from https://github.com/cmdcolin/maf2bed
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
687 Note: Both formats start with a MAF as input, and note that your MAF file should contain the species name and chromosome name
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
688 e.g. hg38.chr1 in the sequence identifiers.
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
689 need the reference id - eg hg18, for maf2bed.pl as the first parameter
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
690 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
691 tId = trackData["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
692 mafPlugin = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
693 "plugins": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
694 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
695 "name": "MafViewer",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
696 "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
697 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
698 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
699 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
700 categ = trackData["category"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
701 fname = f"{tId}"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
702 dest = os.path.join(self.outdir, fname)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
703 gname = trackData["assemblyNames"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
704
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
705 cmd = [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
706 "bash",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
707 os.path.join(INSTALLED_TO, "convertMAF.sh"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
708 data,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
709 gname,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
710 INSTALLED_TO,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
711 dest,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
712 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
713 self.subprocess_check_call(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
714 mafs = open(data, "r").readlines()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
715 mafss = [x for x in mafs if (x.startswith("s\t") or x.startswith("s "))]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
716 samp = [x.split()[1] for x in mafss if len(x.split()) > 0]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
717 sampu = list(dict.fromkeys(samp))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
718 samples = [x.split(".")[0] for x in sampu]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
719 samples.sort()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
720 if logCommands:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
721 logging.debug(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
722 "$$$$ cmd=%s, mafss=%s samp=%s samples=%s"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
723 % (" ".join(cmd), mafss, samp, samples)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
724 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
725 trackDict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
726 "type": "MafTrack",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
727 "trackId": tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
728 "name": trackData["name"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
729 "category": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
730 categ,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
731 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
732 "adapter": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
733 "type": "MafTabixAdapter",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
734 "samples": samples,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
735 "bedGzLocation": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
736 "uri": fname + ".sorted.bed.gz",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
737 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
738 "index": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
739 "location": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
740 "uri": fname + ".sorted.bed.gz.tbi",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
741 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
742 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
743 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
744 "assemblyNames": [trackData["assemblyNames"]],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
745 "displays": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
746 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
747 "type": "LinearBasicDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
748 "displayId": "%s-LinearBasicDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
749 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
750 {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
751 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
752 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
753 style_json = self._prepare_track_style(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
754 trackDict["style"] = style_json
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
755 self.tracksToAdd[gname].append(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
756 self.trackIdlist.append(tId)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
757 if self.config_json.get("plugins", None):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
758 self.config_json["plugins"].append(mafPlugin[0])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
759 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
760 self.config_json.update(mafPlugin)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
761
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
762 def _blastxml_to_gff3(self, xml, min_gap=10):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
763 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
764 cmd = [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
765 "python",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
766 os.path.join(INSTALLED_TO, "blastxml_to_gapped_gff3.py"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
767 "--trim",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
768 "--trim_end",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
769 "--include_seq",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
770 "--min_gap",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
771 str(min_gap),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
772 xml,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
773 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
774 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
775 gff3_unrebased.close()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
776 logging.debug("### blastxml to gff3 cmd = %s" % " ".join(cmd))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
777 return gff3_unrebased.name
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
778
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
779 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
780 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
781 if "parent" in blastOpts and blastOpts["parent"] != "None":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
782 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
783 cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
784 if blastOpts.get("protein", "false") == "true":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
785 cmd.append("--protein2dna")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
786 cmd.extend([os.path.realpath(blastOpts["parent"]), gff3])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
787 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
788 logging.debug("### gff3rebase cmd = %s" % " ".join(cmd))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
789 gff3_rebased.close()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
790 # Replace original gff3 file
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
791 shutil.copy(gff3_rebased.name, gff3)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
792 os.unlink(gff3_rebased.name)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
793 self.add_gff(gff3, trackData, **kwargs)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
794
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
795 def add_bigwig(self, data, trackData):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
796 tId = trackData["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
797 useuri = trackData["useuri"].lower() == "yes"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
798 if useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
799 url = data
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
800 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
801 url = tId
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
802 # slashes in names cause path trouble
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
803 dest = os.path.join(self.outdir, url)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
804 cmd = ["cp", data, dest]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
805 self.subprocess_check_call(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
806 bwloc = {"uri": url}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
807 categ = trackData["category"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
808 trackDict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
809 "type": "QuantitativeTrack",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
810 "trackId": tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
811 "name": trackData["name"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
812 "category": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
813 categ,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
814 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
815 "assemblyNames": [trackData["assemblyNames"]],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
816 "adapter": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
817 "type": "BigWigAdapter",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
818 "bigWigLocation": bwloc,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
819 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
820 "displays": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
821 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
822 "type": "LinearWiggleDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
823 "displayId": "%s-LinearWiggleDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
824 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
825 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
826 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
827 style_json = self._prepare_track_style(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
828 trackDict["style"] = style_json
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
829 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
830 self.trackIdlist.append(tId)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
831
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
832 def add_bam(self, data, trackData, bam_indexes=None, **kwargs):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
833 tId = trackData["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
834 realFName = trackData["path"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
835 useuri = trackData["useuri"].lower() == "yes"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
836 categ = trackData["category"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
837 if useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
838 url = data
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
839 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
840 fname = tId
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
841 dest = "%s/%s" % (self.outdir, fname)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
842 self.subprocess_check_call(["cp", data, dest])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
843 url = fname
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
844 bindex = fname + ".bai"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
845 bi = bam_indexes.split(",")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
846 bam_index = [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
847 x.split(" ~ ")[1].strip()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
848 for x in bi
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
849 if " ~ " in x and x.split(" ~ ")[0].strip() == realFName
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
850 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
851 logging.debug(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
852 "===realFName=%s got %s as bam_indexes %s as bi, %s for bam_index"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
853 % (realFName, bam_indexes, bi, bam_index)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
854 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
855 if len(bam_index) > 0 and os.path.exists(os.path.realpath(bam_index[0])):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
856 self.subprocess_check_call(["cp", bam_index[0], bindex])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
857 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
858 cmd = ["samtools", "index", "-b", "-o", bindex, data]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
859 self.subprocess_check_call(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
860 trackDict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
861 "type": "AlignmentsTrack",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
862 "trackId": tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
863 "name": trackData["name"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
864 "category": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
865 categ,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
866 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
867 "assemblyNames": [trackData["assemblyNames"]],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
868 "adapter": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
869 "type": "BamAdapter",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
870 "bamLocation": {"uri": url},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
871 "index": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
872 "location": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
873 "uri": bindex,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
874 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
875 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
876 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
877 "displays": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
878 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
879 "type": "LinearAlignmentsDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
880 "displayId": "%s-LinearAlignmentsDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
881 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
882 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
883 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
884 style_json = self._prepare_track_style(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
885 trackDict["style"] = style_json
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
886 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
887 self.trackIdlist.append(tId)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
888
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
889 def add_cram(self, data, trackData, cram_indexes=None, **kwargs):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
890 tId = trackData["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
891 realFName = trackData["path"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
892 categ = trackData["category"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
893 useuri = trackData["useuri"].lower() == "yes"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
894 gsa = self.assmeta.get(trackData["assemblyNames"], None)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
895 if gsa:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
896 genseqad = gsa[0]["genome_sequence_adapter"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
897 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
898 genseqad = "Not found"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
899 logging.warning("No adapter found for cram %s in gsa=%s" % (tId, gsa))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
900 if useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
901 url = data
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
902 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
903 fname = tId
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
904 dest = os.path.join(self.outdir, fname)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
905 url = fname
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
906 self.subprocess_check_call(["cp", data, dest])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
907 ci = cram_indexes.split(",")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
908 cram_index = [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
909 x.split(" ~ ")[1].strip()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
910 for x in ci
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
911 if " ~ " in x and x.split(" ~ ")[0].strip() == realFName
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
912 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
913 logging.debug(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
914 "===realFName=%s got %s as cram_indexes %s as ci, %s for cram_index"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
915 % (realFName, cram_indexes, ci, cram_index)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
916 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
917 if len(cram_index) > 0 and os.path.exists(cram_index[0]):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
918 if not os.path.exists(dest + ".crai"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
919 # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
920 self.subprocess_check_call(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
921 ["cp", os.path.realpath(cram_index[0]), dest + ".crai"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
922 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
923 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
924 cpath = os.path.realpath(dest) + ".crai"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
925 cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
926 self.subprocess_check_call(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
927 trackDict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
928 "type": "AlignmentsTrack",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
929 "trackId": tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
930 "name": trackData["name"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
931 "category": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
932 categ,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
933 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
934 "assemblyNames": [trackData["assemblyNames"]],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
935 "adapter": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
936 "type": "CramAdapter",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
937 "cramLocation": {"uri": url},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
938 "craiLocation": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
939 "uri": url + ".crai",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
940 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
941 "sequenceAdapter": genseqad,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
942 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
943 "displays": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
944 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
945 "type": "LinearAlignmentsDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
946 "displayId": "%s-LinearAlignmentsDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
947 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
948 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
949 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
950 style_json = self._prepare_track_style(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
951 trackDict["style"] = style_json
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
952 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
953 self.trackIdlist.append(tId)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
954
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
955 def add_vcf(self, data, trackData):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
956 tId = trackData["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
957 categ = trackData["category"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
958 useuri = trackData["useuri"].lower() == "yes"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
959 if useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
960 url = data
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
961 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
962 url = tId
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
963 dest = os.path.join(self.outdir, url)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
964 cmd = "bgzip -c %s > %s" % (data, dest)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
965 self.subprocess_popen(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
966 cmd = ["tabix", "-f", "-p", "vcf", dest]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
967 self.subprocess_check_call(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
968 trackDict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
969 "type": "VariantTrack",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
970 "trackId": tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
971 "name": trackData["name"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
972 "assemblyNames": [trackData["assemblyNames"]],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
973 "category": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
974 categ,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
975 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
976 "adapter": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
977 "type": "VcfTabixAdapter",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
978 "vcfGzLocation": {"uri": url},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
979 "index": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
980 "location": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
981 "uri": url + ".tbi",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
982 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
983 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
984 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
985 "displays": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
986 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
987 "type": "LinearVariantDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
988 "displayId": "%s-LinearVariantDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
989 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
990 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
991 "type": "ChordVariantDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
992 "displayId": "%s-ChordVariantDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
993 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
994 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
995 "type": "LinearPairedArcDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
996 "displayId": "%s-LinearPairedArcDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
997 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
998 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
999 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1000 style_json = self._prepare_track_style(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1001 trackDict["style"] = style_json
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1002 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1003 self.trackIdlist.append(tId)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1004
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1005 def _sort_gff(self, data, dest):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1006 # Only index if not already done
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1007 if not os.path.exists(dest):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1008 cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s'" % (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1009 data,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1010 dest,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1011 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1012 self.subprocess_popen(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1013 self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1014
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1015 def _sort_bed(self, data, dest):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1016 # Only index if not already done
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1017 if not os.path.exists(dest):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1018 cmd = "sort -k1,1 -k2,2n '%s' | bgzip -c > '%s'" % (data, dest)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1019 self.subprocess_popen(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1020 cmd = ["tabix", "-f", "-p", "bed", dest]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1021 self.subprocess_check_call(cmd)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1022
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1023 def add_gff(self, data, trackData):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1024 tId = trackData["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1025 useuri = trackData["useuri"].lower() == "yes"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1026 if useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1027 url = trackData["path"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1028 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1029 url = tId + ".gz"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1030 dest = os.path.join(self.outdir, url)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1031 self._sort_gff(data, dest)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1032 categ = trackData["category"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1033 trackDict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1034 "type": "FeatureTrack",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1035 "trackId": tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1036 "name": trackData["name"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1037 "assemblyNames": [trackData["assemblyNames"]],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1038 "category": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1039 categ,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1040 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1041 "adapter": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1042 "type": "Gff3TabixAdapter",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1043 "gffGzLocation": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1044 "uri": url,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1045 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1046 "index": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1047 "location": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1048 "uri": url + ".tbi",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1049 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1050 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1051 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1052 "displays": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1053 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1054 "type": "LinearBasicDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1055 "displayId": "%s-LinearBasicDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1056 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1057 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1058 "type": "LinearArcDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1059 "displayId": "%s-LinearArcDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1060 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1061 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1062 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1063 style_json = self._prepare_track_style(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1064 trackDict["style"] = style_json
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1065 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1066 self.trackIdlist.append(tId)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1067
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1068 def add_bed(self, data, ext, trackData):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1069 tId = trackData["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1070 categ = trackData["category"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1071 useuri = trackData["useuri"].lower() == "yes"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1072 if useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1073 url = data
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1074 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1075 url = tId + ".gz"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1076 dest = os.path.join(self.outdir, url)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1077 self._sort_bed(data, dest)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1078 trackDict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1079 "type": "FeatureTrack",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1080 "trackId": tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1081 "name": trackData["name"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1082 "assemblyNames": [trackData["assemblyNames"]],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1083 "adapter": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1084 "category": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1085 categ,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1086 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1087 "type": "BedTabixAdapter",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1088 "bedGzLocation": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1089 "uri": url,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1090 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1091 "index": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1092 "location": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1093 "uri": url + ".tbi",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1094 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1095 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1096 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1097 "displays": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1098 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1099 "type": "LinearBasicDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1100 "displayId": "%s-LinearBasicDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1101 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1102 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1103 "type": "LinearPileupDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1104 "displayId": "%s-LinearPileupDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1105 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1106 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1107 "type": "LinearArcDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1108 "displayId": "%s-LinearArcDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1109 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1110 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1111 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1112 style_json = self._prepare_track_style(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1113 trackDict["style"] = style_json
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1114 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1115 self.trackIdlist.append(tId)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1116
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1117 def add_paf(self, data, trackData, pafOpts, **kwargs):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1118 tname = trackData["name"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1119 tId = trackData["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1120 url = tId
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1121 useuri = data.startswith("http://") or data.startswith("https://")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1122 if not useuri:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1123 dest = os.path.join(self.outdir, url)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1124 self.symlink_or_copy(os.path.realpath(data), dest)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1125 nrow = self.getNrow(dest)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1126 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1127 url = data
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1128 nrow = self.getNrow(url)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1129 categ = trackData["category"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1130 pg = pafOpts["genome"].split(",")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1131 pgc = [x.strip() for x in pg if x.strip() > ""]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1132 gnomes = [x.split(" ~ ") for x in pgc]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1133 logging.debug("pg=%s, gnomes=%s" % (pg, gnomes))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1134 passnames = [trackData["assemblyNames"]] # always first
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1135 for i, (gpath, gname) in enumerate(gnomes):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1136 # may have been forgotten by user for uri
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1137 if len(gname) == 0:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1138 gn = os.path.basename(gpath)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1139 gname = os.path.splitext(gn)[0]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1140 # trouble from spacey names in command lines avoidance
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1141 if len(gname.split()) > 1:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1142 gname = gname.split()[0]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1143 if gname not in passnames:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1144 passnames.append(gname)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1145 useuri = pafOpts["useuri"] == "true"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1146 if gname not in self.genome_names:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1147 # ignore if already there - eg for duplicates among pafs.
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1148 asstrack, first_contig = self.make_assembly(gpath, gname, useuri)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1149 self.genome_names.append(gname)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1150 self.tracksToAdd[gname] = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1151 self.assemblies.append(asstrack)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1152 self.ass_first_contigs.append(first_contig)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1153 trackDict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1154 "type": "SyntenyTrack",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1155 "trackId": tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1156 "assemblyNames": passnames,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1157 "category": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1158 categ,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1159 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1160 "name": tname,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1161 "adapter": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1162 "type": "PAFAdapter",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1163 "pafLocation": {"uri": url},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1164 "assemblyNames": passnames,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1165 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1166 "displays": [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1167 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1168 "type": "LGVSyntenyDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1169 "displayId": "%s-LGVSyntenyDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1170 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1171 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1172 "type": "DotplotDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1173 "displayId": "%s-DotplotDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1174 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1175 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1176 "type": "LinearComparativeDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1177 "displayId": "%s-LinearComparativeDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1178 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1179 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1180 "type": "LinearBasicDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1181 "displayId": "%s-LinearSyntenyDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1182 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1183 ],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1184 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1185 if nrow > 10000:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1186 style_json = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1187 "type": "LGVSyntenyDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1188 "displayId": "%s-LGVSyntenyDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1189 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1190 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1191 style_json = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1192 "type": "LinearBasicDisplay",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1193 "displayId": "%s-LinearBasicDisplay" % tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1194 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1195 trackDict["style"] = style_json
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1196 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1197 self.trackIdlist.append(tId)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1198
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1199 def process_annotations(self, track):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1200 category = track["category"].replace("__pd__date__pd__", TODAY)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1201 for trackIndex, (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1202 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1203 dataset_ext,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1204 useuri,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1205 track_human_label,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1206 extra_metadata,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1207 ) in enumerate(track["trackfiles"]):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1208 if not dataset_path.strip().startswith("http"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1209 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1210 for key, value in mapped_chars.items():
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1211 track_human_label = track_human_label.replace(value, key)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1212 track_human_label = track_human_label.replace(" ", "_")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1213 outputTrackConfig = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1214 "category": category,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1215 "style": {},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1216 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1217
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1218 # hashData = [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1219 # str(dataset_path),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1220 # track_human_label,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1221 # track["category"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1222 # ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1223 # hashData = "|".join(hashData).encode("utf-8")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1224 # hash_string = hashlib.md5(hashData).hexdigest()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1225
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1226 outputTrackConfig["assemblyNames"] = track["assemblyNames"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1227 outputTrackConfig["key"] = track_human_label
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1228 outputTrackConfig["useuri"] = useuri
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1229 outputTrackConfig["path"] = dataset_path
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1230 outputTrackConfig["ext"] = dataset_ext
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1231 outputTrackConfig["trackset"] = track.get("trackset", {})
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1232 outputTrackConfig["label"] = track["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1233 # outputTrackConfig["label"] = "%s_%i_%s_%s" % (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1234 # dataset_ext,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1235 # trackIndex,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1236 # track_human_label,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1237 # hash_string,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1238 # )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1239
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1240 outputTrackConfig["metadata"] = extra_metadata
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1241 outputTrackConfig["name"] = track_human_label
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1242 if track["label"] in self.trackIdlist:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1243 logging.error(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1244 "### not adding %s already in %s"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1245 % (track["label"], self.trackIdlist)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1246 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1247 yield None
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1248 if dataset_ext in ("gff", "gff3"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1249 self.add_gff(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1250 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1251 outputTrackConfig,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1252 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1253 elif dataset_ext in ("hic", "juicebox_hic"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1254 outputTrackConfig["wasCool"] = False
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1255 self.add_hic(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1256 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1257 outputTrackConfig,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1258 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1259 elif dataset_ext in ("cool", "mcool", "scool"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1260 hic_url = outputTrackConfig["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1261 hic_path = os.path.join(self.outdir, hic_url) + ".hic"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1262 outputTrackConfig["wasCool"] = True
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1263 self.subprocess_check_call(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1264 [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1265 "hictk",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1266 "convert",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1267 "-f",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1268 "--output-fmt",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1269 "hic",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1270 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1271 hic_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1272 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1273 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1274 self.add_hic(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1275 hic_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1276 outputTrackConfig,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1277 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1278 elif dataset_ext in ("bed",):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1279 self.add_bed(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1280 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1281 dataset_ext,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1282 outputTrackConfig,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1283 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1284 elif dataset_ext in ("maf",):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1285 self.add_maf(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1286 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1287 outputTrackConfig,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1288 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1289 elif dataset_ext == "bigwig":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1290 self.add_bigwig(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1291 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1292 outputTrackConfig,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1293 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1294 elif dataset_ext == "bam":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1295 real_indexes = track["conf"]["options"]["bam"]["bam_index"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1296 self.add_bam(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1297 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1298 outputTrackConfig,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1299 bam_indexes=real_indexes,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1300 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1301 elif dataset_ext == "cram":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1302 real_indexes = track["conf"]["options"]["cram"]["cram_index"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1303 self.add_cram(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1304 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1305 outputTrackConfig,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1306 cram_indexes=real_indexes,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1307 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1308 elif dataset_ext == "blastxml":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1309 self.add_blastxml(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1310 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1311 outputTrackConfig,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1312 track["conf"]["options"]["blast"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1313 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1314 elif dataset_ext == "vcf":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1315 self.add_vcf(dataset_path, outputTrackConfig)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1316 elif dataset_ext == "paf":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1317 self.add_paf(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1318 dataset_path,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1319 outputTrackConfig,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1320 track["conf"]["options"]["paf"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1321 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1322 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1323 logging.warning("Do not know how to handle %s", dataset_ext)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1324 # Return non-human label for use in other fields
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1325 yield outputTrackConfig["label"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1326
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1327 def add_default_session(self, default_data):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1328 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1329 default session settings are hard and fragile.
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1330 .add_default_view() and other configuration code adapted from
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1331 https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1332 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1333 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1334 track_types = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1335 with open(self.config_json_file, "r") as config_file:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1336 config_json = json.load(config_file)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1337 if self.config_json:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1338 config_json.update(self.config_json)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1339 if "defaultSession" in config_json:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1340 session_json = config_json["defaultSession"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1341 session_views = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1342 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1343 session_json = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1344 session_views = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1345 for gnome in self.assmeta.keys(): # assemblies have their own tracks
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1346 tracks_data = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1347 for track_conf in self.tracksToAdd[gnome]:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1348 tId = track_conf["trackId"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1349 if tId in default_data[gnome]["visibility"]["default_on"]:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1350 track_types[tId] = track_conf["type"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1351 style_data = default_data[gnome]["style"].get(tId, None)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1352 if not style_data:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1353 logging.debug(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1354 "### No style data for %s in available default data %s"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1355 % (tId, default_data)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1356 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1357 style_data = {"type": "LinearBasicDisplay"}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1358 if "displays" in track_conf:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1359 disp = track_conf["displays"][0]["type"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1360 style_data["type"] = disp
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1361 if track_conf.get("style_labels", None):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1362 # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1363 # TODO move this to per track displays?
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1364 style_data["labels"] = track_conf["style_labels"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1365 tracks_data.append(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1366 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1367 "type": track_types[tId],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1368 "configuration": tId,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1369 "displays": [style_data],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1370 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1371 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1372 view_json = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1373 "type": "LinearGenomeView",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1374 "offsetPx": 0,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1375 "minimized": False,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1376 "tracks": tracks_data,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1377 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1378 first = [x for x in self.ass_first_contigs if x[0] == gnome]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1379 if len(first) > 0:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1380 [gnome, refName, end] = first[0]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1381 start = 0
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1382 end = int(end)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1383 drdict = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1384 "refName": refName,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1385 "start": start,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1386 "end": end,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1387 "reversed": False,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1388 "assemblyName": gnome,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1389 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1390 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1391 ddl = default_data.get("defaultLocation", None)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1392 if ddl:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1393 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1394 # allow commas like 100,000 but ignore as integer
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1395 if loc_match:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1396 refName = loc_match.group(1)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1397 drdict["refName"] = refName
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1398 if loc_match.group(2) > "":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1399 drdict["start"] = int(loc_match.group(2).replace(",", ""))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1400 if loc_match.group(3) > "":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1401 drdict["end"] = int(loc_match.group(3).replace(",", ""))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1402 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1403 logging.info(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1404 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1405 % ddl
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1406 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1407 if drdict.get("refName", None):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1408 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1409 view_json["displayedRegions"] = [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1410 drdict,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1411 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1412 logging.info("@@@ defaultlocation %s for default session" % drdict)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1413 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1414 logging.info(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1415 "@@@ no track location for default session - please add one!"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1416 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1417 session_views.append(view_json)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1418 session_name = default_data.get("session_name", "New session")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1419 for key, value in mapped_chars.items():
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1420 session_name = session_name.replace(value, key)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1421 session_json["name"] = session_name
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1422
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1423 if "views" not in session_json:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1424 session_json["views"] = session_views
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1425 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1426 session_json["views"] += session_views
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1427
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1428 pp = json.dumps(session_views, indent=2)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1429 config_json["defaultSession"] = session_json
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1430 self.config_json.update(config_json)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1431 logging.debug("defaultSession=%s" % (pp))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1432 with open(self.config_json_file, "w") as config_file:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1433 json.dump(self.config_json, config_file, indent=2)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1434
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1435 def add_defsess_to_index(self, data):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1436 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1437 ----------------------------------------------------------
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1438 Add some default session settings: set some assemblies/tracks on/off
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1439
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1440 This allows to select a default view:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1441 - jb type (Linear, Circular, etc)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1442 - default location on an assembly
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1443 - default tracks
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1444 - ...
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1445
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1446 Different methods to do that were tested/discussed:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1447 - using a defaultSession item in config.json: this proved to be difficult:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1448 forced to write a full session block, including hard-coded/hard-to-guess items,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1449 no good way to let Jbrowse2 display a scaffold without knowing its size
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1450 - using JBrowse2 as an embedded React component in a tool-generated html file:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1451 it works but it requires generating js code to actually do what we want = chosing default view, assembly, tracks, ...
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1452 - writing a session-spec inside the config.json file: this is not yet supported as of 2.10.2 (see PR 4148 below)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1453 a session-spec is a kind of simplified defaultSession where you don't need to specify every aspect of the session
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1454 - passing a session-spec through URL params by embedding the JBrowse2 index.html inside an iframe
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1455 we selected this option
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1456
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1457 Xrefs to understand the choices:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1458 https://github.com/GMOD/jbrowse-components/issues/2708
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1459 https://github.com/GMOD/jbrowse-components/discussions/3568
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1460 https://github.com/GMOD/jbrowse-components/pull/4148
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1461 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1462 new_index = "Nothing written"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1463 session_spec = {"views": []}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1464 logging.debug("def ass_first=%s\ndata=%s" % (self.ass_first_contigs, data))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1465 for first_contig in self.ass_first_contigs:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1466 logging.debug("first contig=%s" % self.ass_first_contigs)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1467 [gnome, refName, end] = first_contig
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1468 start = 0
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1469 aview = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1470 "assembly": gnome,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1471 "loc": "{}:{}..{}".format(refName, start, end),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1472 "type": "LinearGenomeView",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1473 "tracks": data[gnome]["tracks"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1474 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1475 session_spec["views"].append(aview)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1476 sess = json.dumps(session_spec, sort_keys=True, indent=2)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1477 new_index = INDEX_TEMPLATE.replace(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
1478 "__SESSION_SPEC__", "&session=spec-{}".format(sess)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1479 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1480
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1481 os.rename(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1482 os.path.join(self.outdir, "index.html"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1483 os.path.join(self.outdir, "index_noview.html"),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1484 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1485
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1486 with open(os.path.join(self.outdir, "index.html"), "w") as nind:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1487 nind.write(new_index)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1488 logging.debug(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1489 "#### add_defsession gnome=%s refname=%s\nsession_spec=%s\nnew_index=%s"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff changeset
1490 % (gnome, refName, sess, new_index)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1491 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1492
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1493 def add_general_configuration(self, data):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1494 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1495 Add some general configuration to the config.json file
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1496 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1497
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1498 config_path = self.config_json_file
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1499 if os.path.exists(config_path):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
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diff changeset
1500 with open(config_path, "r") as config_file:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1501 config_json = json.load(config_file)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff changeset
1502 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1503 config_json = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1504 if self.config_json:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1505 config_json.update(self.config_json)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1506 config_data = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1507
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1508 config_data["disableAnalytics"] = data.get("analytics", "false") == "true"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1509
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1510 config_data["theme"] = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1511 "palette": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1512 "primary": {"main": data.get("primary_color", "#0D233F")},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1513 "secondary": {"main": data.get("secondary_color", "#721E63")},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1514 "tertiary": {"main": data.get("tertiary_color", "#135560")},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1515 "quaternary": {"main": data.get("quaternary_color", "#FFB11D")},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1516 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1517 "typography": {"fontSize": int(data.get("font_size", 10))},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1518 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1519 if not config_json.get("configuration", None):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1520 config_json["configuration"] = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1521 config_json["configuration"].update(config_data)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1522 self.config_json.update(config_json)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1523 with open(config_path, "w") as config_file:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1524 json.dump(self.config_json, config_file, indent=2)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1525
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1526 def clone_jbrowse(self, realclone=False):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1527 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1528 Clone a JBrowse directory into a destination directory.
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1529
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1530 `realclone=true` will use the `jbrowse create` command.
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1531 To allow running on internet-less compute and for reproducibility
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1532 use frozen code with `realclone=false
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1533
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1534 """
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1535 dest = self.outdir
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1536 if realclone:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1537 self.subprocess_check_call(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1538 ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1539 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1540 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1541 shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1542 for fn in [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1543 "asset-manifest.json",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1544 "favicon.ico",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1545 "robots.txt",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1546 "umd_plugin.js",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1547 "version.txt",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1548 "test_data",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1549 ]:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1550 try:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1551 path = os.path.join(dest, fn)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1552 if os.path.isdir(path):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1553 shutil.rmtree(path)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1554 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1555 os.remove(path)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1556 except OSError as e:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1557 log.error("Error: %s - %s." % (e.filename, e.strerror))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1558 shutil.copyfile(os.path.join(INSTALLED_TO, "jb2_webserver.py"), os.path.join(dest, "jb2_webserver.py"))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1559
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1560
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1561 def parse_style_conf(item):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1562 if item.text.lower() in ["false", "true", "yes", "no"]:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1563 return item.text.lower in ("yes", "true")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1564 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1565 return item.text
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1566
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1567
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1568 if __name__ == "__main__":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1569 parser = argparse.ArgumentParser(description="", epilog="")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1570 parser.add_argument("--xml", help="Track Configuration")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1571 parser.add_argument(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1572 "--jbrowse2path", help="Path to JBrowse2 directory in BioContainer or Conda"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1573 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1574 parser.add_argument("--outdir", help="Output directory", default="out")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1575 parser.add_argument("--version", "-V", action="version", version=JB2VER)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1576 args = parser.parse_args()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1577 tree = ET.parse(args.xml)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1578 root = tree.getroot()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1579
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1580 # This should be done ASAP
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1581 GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1582 # Sometimes this comes as `localhost` without a protocol
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1583 if not GALAXY_INFRASTRUCTURE_URL.startswith("http"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1584 # so we'll prepend `http://` and hope for the best. Requests *should*
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1585 # be GET and not POST so it should redirect OK
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1586 GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1587
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1588 jc = JbrowseConnector(outdir=args.outdir, jbrowse2path=args.jbrowse2path)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1589
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1590 default_session_data = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1591 trackI = 0
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1592 for ass in root.findall("assembly"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1593 genomes = [
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1594 {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1595 "path": x.attrib["path"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1596 "label": x.attrib["label"].split(" ")[0].replace(",", ""),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1597 "useuri": x.attrib["useuri"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1598 "meta": metadata_from_node(x.find("metadata")),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1599 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1600 for x in ass.findall("metadata/genomes/genome")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1601 ]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1602 primaryGenome = jc.process_genomes(genomes)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1603 if not default_session_data.get(primaryGenome, None):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1604 default_session_data[primaryGenome] = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1605 "tracks": [],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1606 "style": {},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1607 "style_labels": {},
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1608 "visibility": {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1609 "default_on": [],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1610 "default_off": [],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1611 },
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1612 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1613 for track in ass.find("tracks"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1614 track_conf = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1615 track_conf["trackfiles"] = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1616 track_conf["assemblyNames"] = primaryGenome
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1617 is_multi_bigwig = False
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1618 try:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1619 if track.find("options/wiggle/multibigwig") and (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1620 track.find("options/wiggle/multibigwig").text == "True"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1621 ):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1622 is_multi_bigwig = True
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1623 multi_bigwig_paths = []
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1624 except KeyError:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1625 pass
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1626
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1627 trackfiles = track.findall("files/trackFile")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1628 if trackfiles:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1629 for x in trackfiles:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1630 track_conf["label"] = "%s_%d" % (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1631 x.attrib["label"].replace(" ", "_").replace(",", ""),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1632 trackI,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1633 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1634 trackI += 1
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1635 track_conf["useuri"] = x.attrib["useuri"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1636 if is_multi_bigwig:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1637 multi_bigwig_paths.append(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1638 (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1639 track_conf["label"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1640 track_conf["useuri"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1641 os.path.realpath(x.attrib["path"]),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1642 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1643 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1644 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1645 if trackfiles:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1646 metadata = metadata_from_node(x.find("metadata"))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1647 track_conf["dataset_id"] = metadata.get(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1648 "dataset_id", "None"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1649 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1650 if x.attrib["useuri"].lower() == "yes":
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1651 tfa = (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1652 x.attrib["path"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1653 x.attrib["ext"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1654 x.attrib["useuri"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1655 track_conf["label"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1656 metadata,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1657 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1658 else:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1659 tfa = (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1660 os.path.realpath(x.attrib["path"]),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1661 x.attrib["ext"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1662 x.attrib["useuri"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1663 track_conf["label"],
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1664 metadata,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1665 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1666 track_conf["trackfiles"].append(tfa)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1667
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1668 if is_multi_bigwig:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1669 metadata = metadata_from_node(x.find("metadata"))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1670
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1671 track_conf["trackfiles"].append(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1672 (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1673 multi_bigwig_paths, # Passing an array of paths to represent as one track
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1674 "bigwig_multiple",
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1675 "MultiBigWig", # Giving an hardcoded name for now
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1676 {}, # No metadata for multiple bigwig
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1677 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1678 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1679
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1680 track_conf["category"] = track.attrib["cat"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1681 track_conf["format"] = track.attrib["format"]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1682 track_conf["conf"] = etree_to_dict(track.find("options"))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1683 keys = jc.process_annotations(track_conf)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1684 if keys:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1685 for key in keys:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1686 vis = track.attrib.get("visibility", "default_off")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1687 if not vis:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1688 vis = "default_off"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1689 default_session_data[primaryGenome]["visibility"][vis].append(key)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1690 trakdat = jc.tracksToAdd[primaryGenome]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1691 stile = {}
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1692 for trak in trakdat:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1693 if trak["trackId"] == key:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1694 stile = trak.get("style", {})
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1695 if track.find("options/style"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1696 supdate = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1697 item.tag: parse_style_conf(item)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1698 for item in track.find("options/style")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1699 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1700 stile.update(supdate)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1701 default_session_data[primaryGenome]["style"][key] = stile
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1702 if track.find("options/style_labels"):
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1703 default_session_data[primaryGenome]["style_labels"][key] = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1704 item.tag: parse_style_conf(item)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1705 for item in track.find("options/style_labels")
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1706 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1707 default_session_data[primaryGenome]["tracks"].append(key)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1708 default_session_data["defaultLocation"] = root.find(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1709 "metadata/general/defaultLocation"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1710 ).text
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1711 default_session_data["session_name"] = root.find(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1712 "metadata/general/session_name"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1713 ).text
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1714 logging.debug("default_session=%s" % (json.dumps(default_session_data, indent=2)))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1715 jc.zipOut = root.find("metadata/general/zipOut").text == "true"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1716 general_data = {
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1717 "analytics": root.find("metadata/general/analytics").text,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1718 "primary_color": root.find("metadata/general/primary_color").text,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1719 "secondary_color": root.find("metadata/general/secondary_color").text,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1720 "tertiary_color": root.find("metadata/general/tertiary_color").text,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1721 "quaternary_color": root.find("metadata/general/quaternary_color").text,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1722 "font_size": root.find("metadata/general/font_size").text,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1723 }
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1724 jc.add_general_configuration(general_data)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1725 trackconf = jc.config_json.get("tracks", [])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1726 for gnome in jc.genome_names:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1727 gtracks = jc.tracksToAdd[gnome]
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1728 if len(gtracks) > 0:
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1729 logging.debug(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1730 "for genome %s adding gtracks %s"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1731 % (gnome, json.dumps(gtracks, indent=2))
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1732 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1733 trackconf += gtracks
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1734 jc.config_json["tracks"] = trackconf
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1735 assconf = jc.config_json.get("assemblies", [])
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1736 assconf += jc.assemblies
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1737 jc.config_json["assemblies"] = assconf
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1738 logging.debug(
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1739 "assmeta=%s, first_contigs=%s, assemblies=%s, gnames=%s, trackidlist=%s, tracks=%s"
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1740 % (
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1741 jc.assmeta,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1742 jc.ass_first_contigs,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1743 json.dumps(assconf, indent=2),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1744 jc.genome_names,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1745 jc.trackIdlist,
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1746 json.dumps(trackconf, indent=2),
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1747 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1748 )
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1749 jc.write_config()
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1750 jc.add_default_session(default_session_data)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1751 # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called.
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1752 # jc.add_defsess_to_index(default_session_data)
53c2be00bb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff changeset
1753 # jc.text_index() not sure what broke here.