Mercurial > repos > yating-l > jbrowse_hub

comparison TrackHub.py @ 12:e1f188b43750 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Tue, 14 Mar 2017 14:31:36 -0400
parents e7c80e9b70ae
children 8627394693c6
comparison
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11:22efe9f6e8a8 12:e1f188b43750
78 else: 78 else:
79 gff3_file = os.path.join(self.raw, track['fileName']) 79 gff3_file = os.path.join(self.raw, track['fileName'])
80 label = track['fileName'] 80 label = track['fileName']
81 if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf': 81 if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf':
82 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments"}', '--out', self.json]) 82 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments"}', '--out', self.json])
83 elif track['dataType'] == 'gff3-transcript': 83 elif track['dataType'] == 'gff3_transcript':
84 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'MyPlugin/GenePred', '--trackLabel', label, '--config', '{"transcriptType": "transcript"}', '--out', self.json]) 84 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'MyPlugin/GenePred', '--trackLabel', label, '--config', '{"transcriptType": "transcript"}', '--out', self.json])
85 elif track['dataType'] == 'gff3': 85 elif track['dataType'] == 'gff3_mrna':
86 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'MyPlugin/GenePred', '--trackLabel', label, '--out', self.json]) 86 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'MyPlugin/GenePred', '--trackLabel', label, '--out', self.json])
87 else: 87 else:
88 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', self.json]) 88 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', self.json])
89 p.communicate() 89 p.communicate()
90 90