annotate jbrowse.py @ 14:18be2d72fdee draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
author iuc
date Thu, 08 Jun 2017 17:31:38 -0400
parents 69c5e9c0add0
children b5c5470d7c09
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1 #!/usr/bin/env python
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2 import argparse
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3 import codecs
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4 import copy
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5 import hashlib
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6 import json
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7 import logging
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8 import os
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9 import shutil
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10 import struct
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11 import subprocess
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12 import tempfile
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13 import xml.etree.ElementTree as ET
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14 from collections import defaultdict
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15
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16 from Bio.Data import CodonTable
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17
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18 logging.basicConfig(level=logging.INFO)
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19 log = logging.getLogger('jbrowse')
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21
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22 class ColorScaling(object):
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23
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24 COLOR_FUNCTION_TEMPLATE = """
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25 function(feature, variableName, glyphObject, track) {{
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26 var score = {score};
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27 {opacity}
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28 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
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29 }}
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30 """
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31
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32 COLOR_FUNCTION_TEMPLATE_QUAL = """
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33 function(feature, variableName, glyphObject, track) {{
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34 var search_up = function self(sf, attr){{
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35 if(sf.get(attr) !== undefined){{
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36 return sf.get(attr);
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37 }}
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38 if(sf.parent() === undefined) {{
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39 return;
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40 }}else{{
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41 return self(sf.parent(), attr);
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42 }}
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43 }};
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44
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45 var search_down = function self(sf, attr){{
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46 if(sf.get(attr) !== undefined){{
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47 return sf.get(attr);
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48 }}
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49 if(sf.children() === undefined) {{
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50 return;
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51 }}else{{
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52 var kids = sf.children();
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53 for(var child_idx in kids){{
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54 var x = self(kids[child_idx], attr);
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55 if(x !== undefined){{
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56 return x;
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57 }}
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58 }}
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59 return;
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60 }}
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61 }};
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62
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63 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color});
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64 var score = (search_up(feature, 'score') || search_down(feature, 'score'));
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65 {opacity}
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66 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
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67 var red = parseInt(result[1], 16);
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68 var green = parseInt(result[2], 16);
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69 var blue = parseInt(result[3], 16);
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70 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}
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71 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
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72 }}
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73 """
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74
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75 OPACITY_MATH = {
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76 'linear': """
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77 var opacity = (score - ({min})) / (({max}) - ({min}));
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78 """,
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79 'logarithmic': """
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80 var opacity = (score - ({min})) / (({max}) - ({min}));
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81 opacity = Math.log10(opacity) + Math.log10({max});
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82 """,
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83 'blast': """
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84 var opacity = 0;
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85 if(score == 0.0) {
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86 opacity = 1;
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87 } else{
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88 opacity = (20 - Math.log10(score)) / 180;
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89 }
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90 """
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91 }
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92
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93 BREWER_COLOUR_IDX = 0
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94 BREWER_COLOUR_SCHEMES = [
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95 (166, 206, 227),
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96 (31, 120, 180),
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97 (178, 223, 138),
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98 (51, 160, 44),
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99 (251, 154, 153),
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100 (227, 26, 28),
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101 (253, 191, 111),
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102 (255, 127, 0),
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103 (202, 178, 214),
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104 (106, 61, 154),
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105 (255, 255, 153),
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106 (177, 89, 40),
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107 (228, 26, 28),
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108 (55, 126, 184),
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109 (77, 175, 74),
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110 (152, 78, 163),
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111 (255, 127, 0),
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112 ]
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113
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114 BREWER_DIVERGING_PALLETES = {
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115 'BrBg': ("#543005", "#003c30"),
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116 'PiYg': ("#8e0152", "#276419"),
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117 'PRGn': ("#40004b", "#00441b"),
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118 'PuOr': ("#7f3b08", "#2d004b"),
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119 'RdBu': ("#67001f", "#053061"),
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120 'RdGy': ("#67001f", "#1a1a1a"),
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121 'RdYlBu': ("#a50026", "#313695"),
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122 'RdYlGn': ("#a50026", "#006837"),
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123 'Spectral': ("#9e0142", "#5e4fa2"),
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124 }
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125
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126 def __init__(self):
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127 self.brewer_colour_idx = 0
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128
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129 def rgb_from_hex(self, hexstr):
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130 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
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131 return struct.unpack('BBB', codecs.decode(hexstr, 'hex'))
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132
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133 def min_max_gff(self, gff_file):
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134 min_val = None
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135 max_val = None
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136 with open(gff_file, 'r') as handle:
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137 for line in handle:
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138 try:
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139 value = float(line.split('\t')[5])
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140 min_val = min(value, (min_val or value))
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141 max_val = max(value, (max_val or value))
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142
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143 if value < min_val:
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144 min_val = value
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145
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146 if value > max_val:
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147 max_val = value
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148 except Exception:
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149 pass
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150 return min_val, max_val
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151
3
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152 def hex_from_rgb(self, r, g, b):
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153 return '#%02x%02x%02x' % (r, g, b)
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154
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155 def _get_colours(self):
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156 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)]
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157 self.brewer_colour_idx += 1
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158 return r, g, b
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159
8
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160 def parse_menus(self, track):
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161 trackConfig = {'menuTemplate': [{}, {}, {}, {}]}
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162
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163 if 'menu' in track['menus']:
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164 menu_list = [track['menus']['menu']]
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165 if isinstance(track['menus']['menu'], list):
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166 menu_list = track['menus']['menu']
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167
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168 for m in menu_list:
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169 tpl = {
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170 'action': m['action'],
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171 'label': m.get('label', '{name}'),
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172 'iconClass': m.get('iconClass', 'dijitIconBookmark'),
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173 }
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174 if 'url' in m:
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175 tpl['url'] = m['url']
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176 if 'content' in m:
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177 tpl['content'] = m['content']
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178 if 'title' in m:
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179 tpl['title'] = m['title']
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180
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181 trackConfig['menuTemplate'].append(tpl)
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182
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183 return trackConfig
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184
3
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185 def parse_colours(self, track, trackFormat, gff3=None):
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186 # Wiggle tracks have a bicolor pallete
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187 trackConfig = {'style': {}}
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188 if trackFormat == 'wiggle':
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189
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190 trackConfig['style']['pos_color'] = track['wiggle']['color_pos']
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191 trackConfig['style']['neg_color'] = track['wiggle']['color_neg']
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192
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193 if trackConfig['style']['pos_color'] == '__auto__':
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194 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours())
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195 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours())
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196
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197 # Wiggle tracks can change colour at a specified place
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198 bc_pivot = track['wiggle']['bicolor_pivot']
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199 if bc_pivot not in ('mean', 'zero'):
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200 # The values are either one of those two strings
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201 # or a number
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202 bc_pivot = float(bc_pivot)
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203 trackConfig['bicolor_pivot'] = bc_pivot
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204 elif 'scaling' in track:
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205 if track['scaling']['method'] == 'ignore':
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206 if track['scaling']['scheme']['color'] != '__auto__':
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207 trackConfig['style']['color'] = track['scaling']['scheme']['color']
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208 else:
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209 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours())
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210 else:
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211 # Scored method
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212 algo = track['scaling']['algo']
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213 # linear, logarithmic, blast
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214 scales = track['scaling']['scales']
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215 # type __auto__, manual (min, max)
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216 scheme = track['scaling']['scheme']
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217 # scheme -> (type (opacity), color)
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218 # ==================================
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219 # GENE CALLS OR BLAST
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220 # ==================================
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221 if trackFormat == 'blast':
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222 red, green, blue = self._get_colours()
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223 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{
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224 'score': "feature._parent.get('score')",
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225 'opacity': self.OPACITY_MATH['blast'],
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226 'red': red,
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227 'green': green,
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228 'blue': blue,
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229 })
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230 trackConfig['style']['color'] = color_function.replace('\n', '')
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231 elif trackFormat == 'gene_calls':
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232 # Default values, based on GFF3 spec
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233 min_val = 0
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234 max_val = 1000
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235 # Get min/max and build a scoring function since JBrowse doesn't
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236 if scales['type'] == 'automatic' or scales['type'] == '__auto__':
3
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237 min_val, max_val = self.min_max_gff(gff3)
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238 else:
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239 min_val = scales.get('min', 0)
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240 max_val = scales.get('max', 1000)
3
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241
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242 if scheme['color'] == '__auto__':
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243 user_color = 'undefined'
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244 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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245 elif scheme['color'].startswith('#'):
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246 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:]))
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247 auto_color = 'undefined'
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248 else:
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249 user_color = 'undefined'
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250 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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251
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252 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{
8
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253 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}),
3
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254 'user_spec_color': user_color,
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255 'auto_gen_color': auto_color,
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256 })
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257
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258 trackConfig['style']['color'] = color_function.replace('\n', '')
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259 return trackConfig
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260
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261
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262 def etree_to_dict(t):
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263 d = {t.tag: {} if t.attrib else None}
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264 children = list(t)
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265 if children:
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266 dd = defaultdict(list)
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267 for dc in map(etree_to_dict, children):
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268 for k, v in dc.items():
3
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269 dd[k].append(v)
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270 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
3
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271 if t.attrib:
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272 d[t.tag].update(('@' + k, v) for k, v in t.attrib.items())
3
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273 if t.text:
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274 text = t.text.strip()
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275 if children or t.attrib:
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276 if text:
8
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277 d[t.tag]['#text'] = text
3
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278 else:
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279 d[t.tag] = text
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280 return d
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281
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282
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283 # score comes from feature._parent.get('score') or feature.get('score')
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284
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285 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
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286
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287
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288 class JbrowseConnector(object):
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289
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290 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
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291 self.TN_TABLE = {
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292 'gff3': '--gff',
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293 'gff': '--gff',
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294 'bed': '--bed',
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295 'genbank': '--gbk',
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296 }
3
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297
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298 self.cs = ColorScaling()
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299 self.jbrowse = jbrowse
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300 self.outdir = outdir
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301 self.genome_paths = genomes
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302 self.standalone = standalone
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303 self.gencode = gencode
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304 self.tracksToIndex = []
3
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305
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306 if standalone:
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307 self.clone_jbrowse(self.jbrowse, self.outdir)
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308 else:
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309 try:
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310 os.makedirs(self.outdir)
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311 except OSError:
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312 # Ignore if the folder exists
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313 pass
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314
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315 self.process_genomes()
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316 self.update_gencode()
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317
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318 def update_gencode(self):
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319 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]
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320 trackList = os.path.join(self.outdir, 'data', 'trackList.json')
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321 with open(trackList, 'r') as handle:
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322 trackListData = json.load(handle)
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323
3
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324 trackListData['tracks'][0].update({
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325 'codonStarts': table.start_codons,
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326 'codonStops': table.stop_codons,
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327 'codonTable': table.forward_table,
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328 })
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329
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330 with open(trackList, 'w') as handle:
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331 json.dump(trackListData, handle, indent=2)
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332
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333 def subprocess_check_call(self, command):
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334 log.debug('cd %s && %s', self.outdir, ' '.join(command))
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335 subprocess.check_call(command, cwd=self.outdir)
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336
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337 def _jbrowse_bin(self, command):
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338 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
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339
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340 def process_genomes(self):
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341 for genome_path in self.genome_paths:
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342 self.subprocess_check_call([
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343 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
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344 '--fasta', genome_path])
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345
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346 def generate_names(self):
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347 # Generate names
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348
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349 args = [
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350 'perl', self._jbrowse_bin('generate-names.pl'),
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351 '--hashBits', '16'
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352 ]
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353
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354 tracks = ','.join(self.tracksToIndex)
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355
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356 if tracks:
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357 args += ['--tracks', tracks]
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358 else:
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359 # No tracks to index, index only the refseq
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360 args += ['--tracks', 'DNA']
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361
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362 self.subprocess_check_call(args)
3
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363
5
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364 def _add_json(self, json_data):
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365
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366 cmd = [
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367 'perl', self._jbrowse_bin('add-json.pl'),
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368 json.dumps(json_data),
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369 os.path.join('data', 'trackList.json')
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370 ]
3
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371 self.subprocess_check_call(cmd)
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372
3
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373 def _add_track_json(self, json_data):
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374 if len(json_data) == 0:
3
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375 return
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376
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377 tmp = tempfile.NamedTemporaryFile(delete=False)
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378 tmp.write(json.dumps(json_data))
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379 tmp.close()
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380 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name,
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381 os.path.join('data', 'trackList.json')]
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382 self.subprocess_check_call(cmd)
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383 os.unlink(tmp.name)
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384
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385 def _blastxml_to_gff3(self, xml, min_gap=10):
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386 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
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387 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'),
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388 '--trim', '--trim_end', '--min_gap', str(min_gap), xml]
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389 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name)
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390 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
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391 gff3_unrebased.close()
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392 return gff3_unrebased.name
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393
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394 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
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395 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap'])
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396
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397 if 'parent' in blastOpts and blastOpts['parent'] != 'None':
3
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398 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
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399 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')]
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400 if blastOpts.get('protein', 'false') == 'true':
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401 cmd.append('--protein2dna')
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402 cmd.extend([os.path.realpath(blastOpts['parent']), gff3])
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403 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name)
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404 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
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405 gff3_rebased.close()
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406
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407 # Replace original gff3 file
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408 shutil.copy(gff3_rebased.name, gff3)
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409 os.unlink(gff3_rebased.name)
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410
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diff changeset
411 config = {
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412 'glyph': 'JBrowse/View/FeatureGlyph/Segments',
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413 "category": trackData['category'],
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414 }
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415
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416 clientConfig = trackData['style']
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417
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418 cmd = ['perl', self._jbrowse_bin('flatfile-to-json.pl'),
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419 '--gff', gff3,
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parents: 1
diff changeset
420 '--trackLabel', trackData['label'],
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parents: 1
diff changeset
421 '--key', trackData['key'],
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iuc
parents: 1
diff changeset
422 '--clientConfig', json.dumps(clientConfig),
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parents: 1
diff changeset
423 '--config', json.dumps(config),
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parents: 1
diff changeset
424 '--trackType', 'JBrowse/View/Track/CanvasFeatures'
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iuc
parents: 1
diff changeset
425 ]
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parents: 1
diff changeset
426
13
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iuc
parents: 12
diff changeset
427 # className in --clientConfig is ignored, it needs to be set with --className
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
428 if 'className' in trackData['style']:
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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parents: 12
diff changeset
429 cmd += ['--className', trackData['style']['className']]
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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parents: 12
diff changeset
430
3
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parents: 1
diff changeset
431 self.subprocess_check_call(cmd)
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iuc
parents: 1
diff changeset
432 os.unlink(gff3)
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parents: 1
diff changeset
433
8
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iuc
parents: 5
diff changeset
434 if blastOpts.get('index', 'false') == 'true':
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
435 self.tracksToIndex.append("%s" % trackData['label'])
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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436
3
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parents: 1
diff changeset
437 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
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parents: 1
diff changeset
438 dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
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parents: 1
diff changeset
439 cmd = ['ln', data, dest]
1
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parents: 0
diff changeset
440 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
441
12
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diff changeset
442 url = os.path.join('raw', trackData['label'] + '.bw')
3
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parents: 1
diff changeset
443 trackData.update({
12
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diff changeset
444 "urlTemplate": url,
3
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parents: 1
diff changeset
445 "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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parents: 1
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446 "type": "JBrowse/View/Track/Wiggle/Density",
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parents: 1
diff changeset
447 })
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parents: 1
diff changeset
448
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parents: 1
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449 trackData['type'] = wiggleOpts['type']
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parents: 1
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450 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
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parents: 1
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451
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parents: 1
diff changeset
452 if 'min' in wiggleOpts and 'max' in wiggleOpts:
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parents: 1
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453 trackData['min_score'] = wiggleOpts['min']
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parents: 1
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454 trackData['max_score'] = wiggleOpts['max']
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iuc
parents: 1
diff changeset
455 else:
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parents: 1
diff changeset
456 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
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parents: 1
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457
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parents: 1
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458 self._add_track_json(trackData)
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parents: 1
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459
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parents: 1
diff changeset
460 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
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461 dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
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parents: 1
diff changeset
462 cmd = ['ln', '-s', os.path.realpath(data), dest]
1
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iuc
parents: 0
diff changeset
463 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
464
3
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parents: 1
diff changeset
465 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai']
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parents: 1
diff changeset
466 self.subprocess_check_call(cmd)
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parents: 1
diff changeset
467
12
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diff changeset
468 url = os.path.join('raw', trackData['label'] + '.bam')
3
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parents: 1
diff changeset
469 trackData.update({
12
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parents: 11
diff changeset
470 "urlTemplate": url,
1
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iuc
parents: 0
diff changeset
471 "type": "JBrowse/View/Track/Alignments2",
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
472 "storeClass": "JBrowse/Store/SeqFeature/BAM",
3
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parents: 1
diff changeset
473 })
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parents: 1
diff changeset
474
14
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parents: 13
diff changeset
475 # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
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diff changeset
476 # So remove the default 'feature' value for these bam tracks
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
477 if 'className' in trackData['style'] and trackData['style']['className'] == 'feature':
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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parents: 13
diff changeset
478 del trackData['style']['className']
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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parents: 13
diff changeset
479
3
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parents: 1
diff changeset
480 self._add_track_json(trackData)
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parents: 1
diff changeset
481
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parents: 1
diff changeset
482 if bamOpts.get('auto_snp', 'false') == 'true':
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parents: 1
diff changeset
483 trackData2 = copy.copy(trackData)
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parents: 1
diff changeset
484 trackData2.update({
1
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parents: 0
diff changeset
485 "type": "JBrowse/View/Track/SNPCoverage",
3
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parents: 1
diff changeset
486 "key": trackData['key'] + " - SNPs/Coverage",
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff changeset
487 "label": trackData['label'] + "_autosnp",
3
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parents: 1
diff changeset
488 })
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parents: 1
diff changeset
489 self._add_track_json(trackData2)
1
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diff changeset
490
3
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parents: 1
diff changeset
491 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs):
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parents: 1
diff changeset
492 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf')
1
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parents: 0
diff changeset
493 # ln?
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff changeset
494 cmd = ['ln', '-s', data, dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
495 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
496 cmd = ['bgzip', dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
497 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
498 cmd = ['tabix', '-p', 'vcf', dest + '.gz']
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
499 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
500
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 11
diff changeset
501 url = os.path.join('raw', trackData['label'] + '.vcf')
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
502 trackData.update({
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
503 "urlTemplate": url,
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
504 "type": "JBrowse/View/Track/HTMLVariants",
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
505 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
3
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parents: 1
diff changeset
506 })
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parents: 1
diff changeset
507 self._add_track_json(trackData)
1
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parents: 0
diff changeset
508
3
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parents: 1
diff changeset
509 def add_features(self, data, format, trackData, gffOpts, **kwargs):
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parents: 1
diff changeset
510 cmd = [
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parents: 1
diff changeset
511 'perl', self._jbrowse_bin('flatfile-to-json.pl'),
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parents: 1
diff changeset
512 self.TN_TABLE.get(format, 'gff'),
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parents: 1
diff changeset
513 data,
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parents: 1
diff changeset
514 '--trackLabel', trackData['label'],
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parents: 1
diff changeset
515 '--key', trackData['key']
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parents: 1
diff changeset
516 ]
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
517
13
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parents: 12
diff changeset
518 # className in --clientConfig is ignored, it needs to be set with --className
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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parents: 12
diff changeset
519 if 'className' in trackData['style']:
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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parents: 12
diff changeset
520 cmd += ['--className', trackData['style']['className']]
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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parents: 12
diff changeset
521
3
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parents: 1
diff changeset
522 config = copy.copy(trackData)
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parents: 1
diff changeset
523 clientConfig = trackData['style']
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parents: 1
diff changeset
524 del config['style']
1
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parents: 0
diff changeset
525
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
526 if 'match' in gffOpts:
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
527 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
3
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parents: 1
diff changeset
528 cmd += ['--type', gffOpts['match']]
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
529
3
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parents: 1
diff changeset
530 cmd += ['--clientConfig', json.dumps(clientConfig),
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
531 ]
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
532
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
533 trackType = 'JBrowse/View/Track/CanvasFeatures'
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
534 if 'trackType' in gffOpts:
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
535 trackType = gffOpts['trackType']
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
536
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
537 if trackType == 'JBrowse/View/Track/CanvasFeatures':
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
538 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
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parents: 8
diff changeset
539 config['transcriptType'] = gffOpts['transcriptType']
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
540 if 'subParts' in gffOpts and gffOpts['subParts']:
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
541 config['subParts'] = gffOpts['subParts']
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
542 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
543 config['impliedUTRs'] = gffOpts['impliedUTRs']
13
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iuc
parents: 12
diff changeset
544 elif trackType == 'JBrowse/View/Track/HTMLFeatures':
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
545 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
546 cmd += ['--type', gffOpts['transcriptType']]
10
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iuc
parents: 8
diff changeset
547
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
548 cmd += [
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
549 '--trackType', gffOpts['trackType']
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
550 ]
1
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iuc
parents: 0
diff changeset
551
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
552 cmd.extend(['--config', json.dumps(config)])
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
553
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
554 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
555
8
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iuc
parents: 5
diff changeset
556 if gffOpts.get('index', 'false') == 'true':
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
557 self.tracksToIndex.append("%s" % trackData['label'])
3
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parents: 1
diff changeset
558
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parents: 1
diff changeset
559 def process_annotations(self, track):
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iuc
parents: 1
diff changeset
560 outputTrackConfig = {
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
561 'style': {
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
562 'label': track['style'].get('label', 'description'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
563 'className': track['style'].get('className', 'feature'),
3
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iuc
parents: 1
diff changeset
564 'description': track['style'].get('description', ''),
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iuc
parents: 1
diff changeset
565 },
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
566 'category': track['category'],
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
567 }
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iuc
parents: 1
diff changeset
568
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parents: 1
diff changeset
569 for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
570 log.info('Processing %s / %s', track['category'], track_human_label)
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parents: 1
diff changeset
571 outputTrackConfig['key'] = track_human_label
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
572 hashData = [dataset_path, track_human_label, track['category']]
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
573 outputTrackConfig['label'] = hashlib.md5('|'.join(hashData).encode('utf-8')).hexdigest() + '_%s' % i
3
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iuc
parents: 1
diff changeset
574
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iuc
parents: 1
diff changeset
575 # Colour parsing is complex due to different track types having
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
576 # different colour options.
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parents: 1
diff changeset
577 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
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parents: 1
diff changeset
578 # This used to be done with a dict.update() call, however that wiped out any previous style settings...
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iuc
parents: 1
diff changeset
579 for key in colourOptions:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
580 if key == 'style':
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
581 for subkey in colourOptions['style']:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
582 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
583 else:
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iuc
parents: 1
diff changeset
584 outputTrackConfig[key] = colourOptions[key]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
585
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db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
586 if 'menus' in track['conf']['options']:
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
587 menus = self.cs.parse_menus(track['conf']['options'])
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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parents: 11
diff changeset
588 outputTrackConfig.update(menus)
8
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iuc
parents: 5
diff changeset
589
5
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parents: 3
diff changeset
590 # import pprint; pprint.pprint(track)
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diff changeset
591 # import sys; sys.exit()
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parents: 1
diff changeset
592 if dataset_ext in ('gff', 'gff3', 'bed'):
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parents: 1
diff changeset
593 self.add_features(dataset_path, dataset_ext, outputTrackConfig,
8
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iuc
parents: 5
diff changeset
594 track['conf']['options']['gff'])
3
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parents: 1
diff changeset
595 elif dataset_ext == 'bigwig':
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parents: 1
diff changeset
596 self.add_bigwig(dataset_path, outputTrackConfig,
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parents: 1
diff changeset
597 track['conf']['options']['wiggle'])
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parents: 1
diff changeset
598 elif dataset_ext == 'bam':
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parents: 1
diff changeset
599 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
600 if not isinstance(real_indexes, list):
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iuc
parents: 1
diff changeset
601 # <bam_indices>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
602 # <bam_index>/path/to/a.bam.bai</bam_index>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
603 # </bam_indices>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
604 #
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
605 # The above will result in the 'bam_index' key containing a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
606 # string. If there are two or more indices, the container
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
607 # becomes a list. Fun!
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
608 real_indexes = [real_indexes]
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iuc
parents: 1
diff changeset
609
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parents: 1
diff changeset
610 self.add_bam(dataset_path, outputTrackConfig,
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parents: 1
diff changeset
611 track['conf']['options']['pileup'],
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
612 bam_index=real_indexes[i])
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iuc
parents: 1
diff changeset
613 elif dataset_ext == 'blastxml':
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iuc
parents: 1
diff changeset
614 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
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iuc
parents: 1
diff changeset
615 elif dataset_ext == 'vcf':
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
616 self.add_vcf(dataset_path, outputTrackConfig)
1
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parents: 0
diff changeset
617
5
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parents: 3
diff changeset
618 # Return non-human label for use in other fields
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
619 yield outputTrackConfig['label']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
620
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
621 def add_final_data(self, data):
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
622 viz_data = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
623 if len(data['visibility']['default_on']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
624 viz_data['defaultTracks'] = ','.join(data['visibility']['default_on'])
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parents: 3
diff changeset
625
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
626 if len(data['visibility']['always']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
627 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always'])
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parents: 3
diff changeset
628
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
629 if len(data['visibility']['force']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
630 viz_data['forceTracks'] = ','.join(data['visibility']['force'])
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parents: 3
diff changeset
631
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parents: 3
diff changeset
632 generalData = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
633 if data['general']['aboutDescription'] is not None:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
634 generalData['aboutThisBrowser'] = {'description': data['general']['aboutDescription'].strip()}
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parents: 3
diff changeset
635
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
636 generalData['view'] = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
637 'trackPadding': data['general']['trackPadding']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
638 }
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
639 generalData['shareLink'] = (data['general']['shareLink'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
640 generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
641 generalData['show_nav'] = (data['general']['show_nav'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
642 generalData['show_overview'] = (data['general']['show_overview'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
643 generalData['show_menu'] = (data['general']['show_menu'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
644 generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
645
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
646 viz_data.update(generalData)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
647 self._add_json(viz_data)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
648
1
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parents: 0
diff changeset
649 def clone_jbrowse(self, jbrowse_dir, destination):
3
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diff changeset
650 """Clone a JBrowse directory into a destination directory.
7342f467507b Uploaded v0.4 of JBrowse
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651 """
1
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parents: 0
diff changeset
652 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
653 # unlike copytree
3
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654 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination]
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diff changeset
655 log.debug(' '.join(cmd))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff changeset
656 subprocess.check_call(cmd)
3
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657 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')]
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diff changeset
658 log.debug(' '.join(cmd))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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659 subprocess.check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
660
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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661 # http://unix.stackexchange.com/a/38691/22785
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
662 # JBrowse releases come with some broken symlinks
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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663 cmd = ['find', destination, '-type', 'l', '-xtype', 'l', '-exec', 'rm', "'{}'", '+']
3
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parents: 1
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664 log.debug(' '.join(cmd))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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665 subprocess.check_call(cmd)
0
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diff changeset
666
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
667
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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668 if __name__ == '__main__':
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
669 parser = argparse.ArgumentParser(description="", epilog="")
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670 parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration')
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff changeset
671
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
672 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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673 parser.add_argument('--outdir', help='Output directory', default='out')
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diff changeset
674 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
675 args = parser.parse_args()
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
676
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677 tree = ET.parse(args.xml.name)
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
678 root = tree.getroot()
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679
1
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iuc
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diff changeset
680 jc = JbrowseConnector(
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff changeset
681 jbrowse=args.jbrowse,
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff changeset
682 outdir=args.outdir,
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
683 genomes=[os.path.realpath(x.text) for x in root.findall('metadata/genomes/genome')],
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
684 standalone=args.standalone,
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
685 gencode=root.find('metadata/gencode').text
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
686 )
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
687
5
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diff changeset
688 extra_data = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
689 'visibility': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
690 'default_on': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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691 'default_off': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
692 'force': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
693 'always': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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694 },
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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695 'general': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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696 'defaultLocation': root.find('metadata/general/defaultLocation').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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697 'trackPadding': int(root.find('metadata/general/trackPadding').text),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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698 'shareLink': root.find('metadata/general/shareLink').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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699 'aboutDescription': root.find('metadata/general/aboutDescription').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
700 'show_tracklist': root.find('metadata/general/show_tracklist').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
701 'show_nav': root.find('metadata/general/show_nav').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
702 'show_overview': root.find('metadata/general/show_overview').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
703 'show_menu': root.find('metadata/general/show_menu').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
704 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
705 }
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
706 }
3
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diff changeset
707 for track in root.findall('tracks/track'):
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708 track_conf = {}
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709 track_conf['trackfiles'] = [
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
710 (os.path.realpath(x.attrib['path']), x.attrib['ext'], x.attrib['label'])
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diff changeset
711 for x in track.findall('files/trackFile')
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
712 ]
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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713
3
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diff changeset
714 track_conf['category'] = track.attrib['cat']
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diff changeset
715 track_conf['format'] = track.attrib['format']
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diff changeset
716 try:
7342f467507b Uploaded v0.4 of JBrowse
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717 # Only pertains to gff3 + blastxml. TODO?
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diff changeset
718 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff changeset
719 except TypeError:
3
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diff changeset
720 track_conf['style'] = {}
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
721 pass
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
722 track_conf['conf'] = etree_to_dict(track.find('options'))
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
723 keys = jc.process_annotations(track_conf)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
724
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff changeset
725 for key in keys:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
726 extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
727
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
728 jc.add_final_data(extra_data)
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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729 jc.generate_names()