Mercurial > repos > yating-l > jbrowse_hub
comparison TrackHub.py @ 45:15b4a74722d1 draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 73ede51a133dc8914812195a1b4cd512bfb8f23d
| author | yating-l |
|---|---|
| date | Wed, 22 Mar 2017 12:07:32 -0400 |
| parents | 37422f705e9b |
| children | 6803152ea92a |
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| 44:37422f705e9b | 45:15b4a74722d1 |
|---|---|
| 43 p.communicate() | 43 p.communicate() |
| 44 except OSError as e: | 44 except OSError as e: |
| 45 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror) | 45 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror) |
| 46 #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings | 46 #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings |
| 47 def addTrack(self, track): | 47 def addTrack(self, track): |
| 48 print "false_path" , track['false_path'] | 48 #print "false_path" , track['false_path'] |
| 49 if track['false_path'] in self.metaData.keys(): | 49 if track['false_path'] in self.metaData.keys(): |
| 50 metadata = self.metaData[track['false_path']] | 50 metadata = self.metaData[track['false_path']] |
| 51 else: | 51 else: |
| 52 metadata = {} | 52 metadata = {} |
| 53 self.SetMetadata(track, metadata) | 53 self.SetMetadata(track, metadata) |
| 56 # print "add bam track\n" | 56 # print "add bam track\n" |
| 57 elif track['dataType'] == 'bigwig': | 57 elif track['dataType'] == 'bigwig': |
| 58 self.BigWig(track, metadata) | 58 self.BigWig(track, metadata) |
| 59 else: | 59 else: |
| 60 gff3_file = os.path.join(self.raw, track['fileName']) | 60 gff3_file = os.path.join(self.raw, track['fileName']) |
| 61 if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf': | 61 if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf' or track['dataType'] == 'blastxml': |
| 62 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_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]) | 62 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_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]) |
| 63 elif track['dataType'] == 'gff3_transcript': | 63 elif track['dataType'] == 'gff3_transcript': |
| 64 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"transcriptType": "transcript", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json]) | 64 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"transcriptType": "transcript", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json]) |
| 65 else: | 65 else: |
| 66 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json]) | 66 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json]) |
| 126 bigwig_track['category'] = metadata['category'] | 126 bigwig_track['category'] = metadata['category'] |
| 127 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks') | 127 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks') |
| 128 | 128 |
| 129 #If the metadata is not set, use the default value | 129 #If the metadata is not set, use the default value |
| 130 def SetMetadata(self, track, metadata): | 130 def SetMetadata(self, track, metadata): |
| 131 print metadata | 131 #print metadata |
| 132 #track.update(metadata) | 132 #track.update(metadata) |
| 133 if 'label' not in metadata.keys() or metadata['label'] == '': | 133 if 'label' not in metadata.keys() or metadata['label'] == '': |
| 134 metadata['label'] = track['fileName'] | 134 metadata['label'] = track['fileName'] |
| 135 if 'color' not in metadata.keys() or metadata['color'] == '': | 135 if 'color' not in metadata.keys() or metadata['color'] == '': |
| 136 metadata['color'] = "#daa520" | 136 metadata['color'] = "#daa520" |