Mercurial > repos > yating-l > jbrowsearchivecreator

comparison TrackHub.py @ 47:1eb4adefd747 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 97a743ee6d228c8a0a5778ec3cb6f68a2e22c8e3
author yating-l
date Tue, 19 Jun 2018 17:39:12 -0400
parents 061da5d3a219
children 804e7217f27c
comparison
equal deleted inserted replaced
46:061da5d3a219 47:1eb4adefd747
54 self.nameIndexTrackList = [] 54 self.nameIndexTrackList = []
55 55
56 56
57 def addTrack(self, trackDbObject): 57 def addTrack(self, trackDbObject):
58 if trackDbObject['nameIndex'] == "true": 58 if trackDbObject['nameIndex'] == "true":
59 self.nameIndexTracksList.append(trackDbObject['trackLabel']) 59 self.nameIndexTrackList.append(trackDbObject['trackLabel'])
60 if trackDbObject['dataType'].lower() == 'bam': 60 if trackDbObject['dataType'].lower() == 'bam':
61 subtools.add_track_json(self.trackList, trackDbObject['options']) 61 subtools.add_track_json(self.trackList, trackDbObject['options'])
62 elif trackDbObject['dataType'].lower() == 'bigwig': 62 elif trackDbObject['dataType'].lower() == 'bigwig':
63 subtools.add_track_json(self.trackList, trackDbObject['options']) 63 subtools.add_track_json(self.trackList, trackDbObject['options'])
64 else: 64 else:
104 104
105 def _prepareRefseq(self): 105 def _prepareRefseq(self):
106 subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath) 106 subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)
107 107
108 def _indexName(self): 108 def _indexName(self):
109 subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList) 109 if self.nameIndexTrackList:
110 print "finished name index \n" 110 subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList)
111 print "finished name index \n"
111 112
112 def _outHtml(self): 113 def _outHtml(self):
113 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')], 114 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
114 output_encoding='utf-8', encoding_errors='replace') 115 output_encoding='utf-8', encoding_errors='replace')
115 htmlTemplate = mylookup.get_template("display.txt") 116 htmlTemplate = mylookup.get_template("display.txt")