Mercurial > repos > fubar > jbrowse2
annotate autogenJB2.py @ 113:878c27dfea9d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 45375b64cbc99173525a2b374d71a13e650ce1b0
author | bgruening |
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date | Sun, 28 Jul 2024 02:42:43 +0000 |
parents | b1260bca5fdc |
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rev | line source |
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8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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1 import argparse |
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15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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2 import logging |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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3 import os |
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8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
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4 import sys |
8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
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5 |
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15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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6 from jbrowse2 import JbrowseConnector as jbC |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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7 |
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cefe9dbf1d80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
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8 |
cefe9dbf1d80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
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9 logging.basicConfig(level=logging.DEBUG) |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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10 log = logging.getLogger("jbrowse") |
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8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
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11 |
8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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12 if __name__ == "__main__": |
8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
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13 parser = argparse.ArgumentParser(description="", epilog="") |
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15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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14 parser.add_argument("--sessName", help="Session name", default="AutoJBrowse") |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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15 parser.add_argument( |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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16 "--trackmeta", |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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17 help="Repeatable 'filename,filext,filepath,[bai/crai path for filesystem bam/cram]' for JBrowse2 tracks", |
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15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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18 default=[], |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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19 action="append", |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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20 ) |
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8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
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21 parser.add_argument( |
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15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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22 "--referencemeta", |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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23 help="Repeatable 'filename, filext, filepath, ... ,' for JBrowse2 reference tracks - usually only one needed", |
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8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
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24 default=[], |
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15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
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25 action="append", |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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26 ) |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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27 parser.add_argument( |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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28 "--pafmeta", |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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29 help="Repeatable. Each is a 'pafname, filext, filepath, ... ,' for a JBrowse2 paf track", |
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15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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30 default=[], |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
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31 action="append", |
30
8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
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32 ) |
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15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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33 parser.add_argument( |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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34 "--pafreferencemeta", |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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35 help="Repeatable. Each is a 'pafname,refpath,refname' Every pafname must have one or more", |
35
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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36 default=[], |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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37 action="append", |
15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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38 ) |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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39 parser.add_argument( |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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40 "--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda" |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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41 ) |
39
bc57164eb270
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661
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42 parser.add_argument("--outdir", help="Output directory", required=True) |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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43 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2") |
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8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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44 args = parser.parse_args() |
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15da358c3108
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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45 sessName = args.sessName |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
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46 default_session_data = {} |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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47 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key' |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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48 trackList = [x.strip().split(",") for x in args.trackmeta if x > ""] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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49 refList = [x.strip().split(",") for x in args.referencemeta if x > ""] |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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50 if len(refList) > 0: |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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51 listgenomes = [f for f in refList if f[1] in ["fasta", "fasta.gz"]] |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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52 # assume no pafs here |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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53 if len(listgenomes) > 0: |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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54 genome_paths = [x[0] for x in listgenomes] |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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55 genome_names = [x[2] for x in listgenomes] |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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56 guseuri = [] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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57 for x in genome_paths: |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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58 if x.startswith("http://") or x.startswith("https://"): |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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59 guseuri.append("yes") |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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60 else: |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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61 guseuri.append("no") |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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62 jc = jbC( |
8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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63 outdir=args.outdir, |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661
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64 jbrowse2path=args.jbrowse2path, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
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65 ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
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66 genomes = ( |
cefe9dbf1d80
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
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67 [ |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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68 { |
8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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69 "path": x, |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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70 "label": genome_names[i], |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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71 "useuri": guseuri[i], |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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72 "meta": { |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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73 "name": genome_names[i], |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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74 "dataset_dname": genome_names[i], |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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75 }, |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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76 } |
8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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77 for i, x in enumerate(genome_paths) |
8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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78 ], |
67
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
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79 ) |
62
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80 assref_name = jc.process_genomes(genomes[0]) |
77
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81 if not default_session_data.get(assref_name, None): |
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82 default_session_data[assref_name] = { |
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83 "tracks": [], |
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84 "style": {}, |
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85 "style_labels": {}, |
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86 "visibility": { |
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87 "default_on": [], |
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88 "default_off": [], |
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89 }, |
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90 } |
35
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91 listtracks = trackList |
98
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92 # foo.paf must have a foo_paf.fasta or fasta.gz to match |
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93 tnames = [x[2] for x in listtracks] |
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94 texts = [x[1] for x in listtracks] |
113
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95 if len(listtracks) == 0: |
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96 sys.stderr.write( |
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97 "Please add at least one track (bam,bed,bigwig,blastxml,cram,gff,hic,maf,paf or vcf) to the collection. No suitable track files for autogenJB2 - nothing to process" |
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98 ) |
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99 sys.exit(5) |
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100 for i, track in enumerate(listtracks): |
67
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101 track_conf = { |
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102 "trackfiles": [], |
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103 "category": "autogenerated", |
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104 "assemblyNames": assref_name, |
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105 } |
35
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106 tpath, trext, trackname = track[:3] |
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107 track_conf["dataset_id"] = trackname |
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108 useuri = "no" |
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109 if tpath.startswith("http://") or tpath.startswith("https://"): |
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110 useuri = "yes" |
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111 if trext == "paf": |
98
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112 refname = trackname + "_paf.fasta" |
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113 refdat = [x[2] for x in listtracks if x[2] == refname] |
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114 if not refdat: |
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115 jc.logging.warn( |
98
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116 "No reference file %s corresponding to paf file %s found. Not building - there must be a corresponding fasta for each paf" |
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117 % (refname, trackname) |
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118 ) |
98
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119 sys.exit(3) |
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120 else: |
57
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121 track_conf.update( |
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122 { |
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123 "conf": { |
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124 "options": { |
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125 "paf": { |
98
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126 "genome": refdat, |
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127 "genome_label": trackname, |
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128 } |
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129 } |
30
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130 } |
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131 } |
57
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132 ) |
46
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133 elif trext == "bam": |
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134 ipath = track[3] |
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135 if not os.path.exists(ipath): |
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136 ipath = os.path.realpath( |
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137 os.path.join(jc.outdir, trackname + ".bai") |
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138 ) |
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139 cmd = [ |
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140 "samtools", |
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141 "index", |
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142 "-b", |
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143 "-o", |
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144 ipath, |
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145 os.path.realpath(track[0]), |
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146 ] |
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147 sys.stdout.write("#### calling %s" % " ".join(cmd)) |
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148 jc.subprocess_check_call(cmd) |
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149 track_conf.update( |
98
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150 {"conf": {"options": {"bam": {"bam_index": " %s ~ %s," % (tpath, ipath)}}}} |
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151 ) |
46
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152 elif trext == "cram": |
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153 ipath = track[3] |
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154 if not os.path.exists(ipath): |
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155 ipath = os.path.realpath( |
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156 os.path.join("./", trackname + ".crai") |
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157 ) |
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158 cmd = [ |
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159 "samtools", |
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160 "index", |
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161 "-c", |
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162 "-o", |
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163 ipath, |
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164 os.path.realpath(track[0]), |
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165 ] |
46
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166 jc.subprocess_check_call(cmd) |
57
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167 track_conf.update( |
93
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168 {"conf": {"options": {"cram": {"cram_index": "%s ~ %s," % (tpath, ipath)}}}} |
57
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169 ) |
48
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170 track_conf["path"] = tpath |
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171 track_conf["format"] = trext |
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172 track_conf["name"] = trackname |
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173 track_conf["label"] = trackname |
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174 track_conf["trackfiles"].append((tpath, trext, useuri, trackname, {})) |
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175 keys = jc.process_annotations(track_conf) |
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176 |
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177 if keys: |
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178 for key in keys: |
46
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179 if trext in [ |
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180 "bigwig", |
67
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181 "gff", |
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182 "gff3", |
46
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183 "vcf", |
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184 "maf", |
72
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185 "bed", |
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186 "hic" |
46
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187 ]: |
77
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188 default_session_data[assref_name]["visibility"]["default_on"].append(key) |
35
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189 else: |
77
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190 default_session_data[assref_name]["visibility"]["default_off"].append( |
46
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191 key |
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192 ) |
60
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193 if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]: |
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194 ttype = "LinearBasicDisplay" |
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195 if trext == "vcf": |
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196 ttype = "LinearVariantDisplay" |
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197 style_json = { |
67
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198 "type": ttype, |
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199 "trackShowLabels": False, |
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200 "trackShowDescriptions": False, |
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201 } |
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202 default_session_data[assref_name]["style"][key] = style_json |
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203 default_session_data[assref_name]["tracks"].append(key) |
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204 # general_data = { |
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205 # "analytics": root.find("metadata/general/analytics").text, |
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206 # "primary_color": root.find("metadata/general/primary_color").text, |
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207 # "secondary_color": root.find("metadata/general/secondary_color").text, |
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208 # "tertiary_color": root.find("metadata/general/tertiary_color").text, |
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209 # "quaternary_color": root.find("metadata/general/quaternary_color").text, |
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210 # "font_size": root.find("metadata/general/font_size").text, |
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211 # } |
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212 jc.add_general_configuration({}) |
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213 trackconf = jc.config_json.get("tracks", []) |
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214 for gnome in jc.genome_names: |
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215 trackconf += jc.tracksToAdd[gnome] |
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216 logging.debug( |
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217 "++++ adding trackconf=%s for gnome %s" % (trackconf, gnome) |
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218 ) |
65
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219 jc.config_json["tracks"] = trackconf |
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220 assconf = jc.config_json.get("assemblies", []) |
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221 assconf += jc.assemblies |
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222 jc.config_json["assemblies"] = assconf |
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223 logging.debug("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names)) |
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224 jc.write_config() |
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225 default_session_data.update({"session_name": sessName}) |
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226 track_conf.update(default_session_data) |
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227 jc.add_default_session(default_session_data) |
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228 # jc.add_defsess_to_index(default_session_data) |
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229 # jc.text_index() not sure what broke here. |
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230 else: |
46
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231 sys.stderr.write( |
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232 "Please add a fasta genome reference to the collection. No suitable reference fasta for autogenJB2 - nothing to process" |
46
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233 ) |