Mercurial > repos > yating-l > jbrowsearchivecreator

annotate TrackHub.py @ 16:a377a3afe210 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 594c5fa1e3cdb378ecf6b5490ec2cbac5fa8a61e-dirty
author yating-l
date Wed, 05 Jul 2017 16:04:19 -0400
parents cdc32923786d
children 466d52f83079
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8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1 #!/usr/bin/env python
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yating-l
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2
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3 import os
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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4 import subprocess
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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5 import shutil
10
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6 import zipfile
0
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7 import json
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8 import utils
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9
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10
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11 class TrackHub:
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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12 def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData, jbrowse_host):
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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13 self.input_files = inputFiles.tracks
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14 self.outfile = outputDirect
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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15 self.outfolder = extra_files_path
13
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16 self.out_path = os.path.join(extra_files_path, 'myHub')
0
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17 self.reference = reference
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18 self.tool_dir = tool_dir
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19 self.metaData = metaData
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20 self.raw = os.path.join(self.out_path, 'raw')
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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21 self.json = os.path.join(self.out_path, 'json')
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22 self.jbrowse_host = jbrowse_host
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23 try:
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24 if os.path.exists(self.json):
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25 shutil.rmtree(self.json)
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26 os.makedirs(self.json)
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27 except OSError as e:
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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28 print "Cannot create json folder error({0}): {1}".format(e.errno, e.strerror)
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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29 else:
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30 print "Create jbrowse folder {}".format(self.out_path)
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31
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32 def createHub(self):
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33 self.prepareRefseq()
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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34 for input_file in self.input_files:
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35 self.addTrack(input_file)
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36 self.indexName()
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37 slink = self.makeArchive()
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38 self.outHtml(slink)
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39 print "Success!\n"
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40
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41 def prepareRefseq(self):
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42 try:
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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43 #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
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44 subprocess.call(['prepare-refseqs.pl', '--fasta', self.reference, '--out', self.json])
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45 except OSError as e:
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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46 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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47 #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings
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48 def addTrack(self, track):
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49 #print "false_path" , track['false_path']
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50 if track['false_path'] in self.metaData.keys():
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51 metadata = self.metaData[track['false_path']]
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52 else:
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53 metadata = {}
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54 self.SetMetadata(track, metadata)
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55 if track['dataType'] == 'bam':
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56 self.Bam(track, metadata)
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57 # print "add bam track\n"
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58 elif track['dataType'] == 'bigwig':
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59 self.BigWig(track, metadata)
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60 else:
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61 flat_file = os.path.join(self.raw, track['fileName'])
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62 if track['dataType'] == 'bed':
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63 subprocess.call(['flatfile-to-json.pl', '--bed', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
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64 elif track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf' or track['dataType'] == 'blastxml':
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65 subprocess.call(['flatfile-to-json.pl', '--gff', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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66 elif track['dataType'] == 'gff3_transcript':
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67 subprocess.call(['flatfile-to-json.pl', '--gff', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"transcriptType": "transcript", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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68 else:
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69 subprocess.call(['flatfile-to-json.pl', '--gff', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
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70
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71 def indexName(self):
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72 subprocess.call(['generate-names.pl', '-v', '--out', self.json])
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73 print "finished name index \n"
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74
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75 def makeArchive(self):
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76 file_dir = os.path.abspath(self.outfile)
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77 source_dir = os.path.dirname(file_dir)
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78 folder_name = os.path.basename(self.outfolder)
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79 source_name = os.path.basename(self.out_path)
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80 source = os.path.join(source_dir, folder_name, source_name)
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81 slink = source.replace('/', '_')
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82 slink = os.path.join('/var/www/html/JBrowse-1.12.1/data', slink)
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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83 try:
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84 if os.path.islink(slink):
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85 os.unlink(slink)
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86 except OSError as oserror:
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87 print "Cannot create symlink to the data({0}): {1}".format(oserror.errno, oserror.strerror)
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88 os.symlink(source, slink)
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89 return slink
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90
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91 def outHtml(self, slink):
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92 with open(self.outfile, 'w') as htmlfile:
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93 htmlstr = 'The JBrowse Hub is created: <br>'
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94 url = self.jbrowse_host + "/JBrowse-1.12.1/index.html?data=%s"
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95 jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub</a></li>' % url
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96 link_name = os.path.basename(slink)
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97 relative_path = os.path.join('data', link_name + '/json')
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98 htmlstr += jbrowse_hub % relative_path
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99 htmlfile.write(htmlstr)
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100
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101 def createTrackList(self):
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102 trackList = os.path.join(self.json, "trackList.json")
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103 if not os.path.exists(trackList):
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104 os.mknod(trackList)
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105
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106 def Bam(self, track, metadata):
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107 #create trackList.json if not exist
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108 self.createTrackList()
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109 json_file = os.path.join(self.json, "trackList.json")
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110 bam_track = dict()
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111 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
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112 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
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113 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
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114 bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index'])
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115 bam_track['label'] = metadata['label']
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116 bam_track['category'] = metadata['category']
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117 bam_track = json.dumps(bam_track)
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118 #Use add-track-json.pl to add bam track to json file
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119 new_track = subprocess.Popen(['echo', bam_track], stdout=subprocess.PIPE)
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120 subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
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121
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122 def BigWig(self, track, metadata):
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123 #create trackList.json if not exist
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124 self.createTrackList()
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125 json_file = os.path.join(self.json, "trackList.json")
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126 bigwig_track = dict()
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127 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
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128 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
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129 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
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130 bigwig_track['label'] = metadata['label']
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131 bigwig_track['style'] = metadata['style']
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132 bigwig_track['category'] = metadata['category']
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133 bigwig_track = json.dumps(bigwig_track)
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134 #Use add-track-json.pl to add bigwig track to json file
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135 new_track = subprocess.Popen(['echo', bigwig_track], stdout=subprocess.PIPE)
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136 #output = new_track.communicate()[0]
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137 subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
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138
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139 #If the metadata is not set, use the default value
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140 def SetMetadata(self, track, metadata):
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141 if 'label' not in metadata.keys() or metadata['label'] == '':
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142 metadata['label'] = track['fileName']
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143 if 'color' not in metadata.keys() or metadata['color'] == '':
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144 metadata['color'] = "#daa520"
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145 if track['dataType'] == 'bigwig':
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146 if 'style' not in metadata.keys():
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147 metadata['style'] = {}
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148 if 'pos_color' not in metadata['style'] or metadata['style']['pos_color'] == '':
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149 metadata['style']['pos_color'] = "#FFA600"
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150 if 'neg_color' not in metadata['style'] or metadata['style']['neg_color'] == '':
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151 metadata['style']['neg_color'] = "#005EFF"
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152 if 'category' not in metadata.keys() or metadata['category'] == '':
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153 metadata['category'] = "Default group"
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154 if track['dataType'] == 'blastxml':
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155 metadata['type'] = "G-OnRamp_plugin/BlastAlignment"
16
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156 if track['dataType'] == 'bigpsl':
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157 metadata['type'] = "G-OnRamp_plugin/BlastAlignment"
0
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158 elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna':
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159 metadata['type'] = "G-OnRamp_plugin/GenePred"
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160 else:
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161 metadata['type'] = "CanvasFeatures"
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162
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163
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164
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165
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166
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167
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168