Mercurial > repos > yating-l > jbrowsearchivecreator

comparison TrackHub.py @ 46:061da5d3a219 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3160592f4119e684ab5843dd28a2e6cf11df0121-dirty
author yating-l
date Tue, 19 Jun 2018 16:28:36 -0400
parents b1553f2a4942
children 1eb4adefd747
comparison
equal deleted inserted replaced
45:d56955fc4c75 46:061da5d3a219
49 self.trackList = os.path.join(self.mySpecieFolderPath, "trackList.json") 49 self.trackList = os.path.join(self.mySpecieFolderPath, "trackList.json")
50 self._createTrackList() 50 self._createTrackList()
51 if Datatype.trackType == 'HTMLFeatures': 51 if Datatype.trackType == 'HTMLFeatures':
52 self.myTrackStyle = TrackStyles(self.tool_directory, self.mySpecieFolderPath, self.trackList) 52 self.myTrackStyle = TrackStyles(self.tool_directory, self.mySpecieFolderPath, self.trackList)
53 self.logger = logging.getLogger(__name__) 53 self.logger = logging.getLogger(__name__)
54 self.nameIndexTrackList = []
54 55
55
56 56
57 def addTrack(self, trackDbObject): 57 def addTrack(self, trackDbObject):
58 if trackDbObject['nameIndex'] == "true":
59 self.nameIndexTracksList.append(trackDbObject['trackLabel'])
58 if trackDbObject['dataType'].lower() == 'bam': 60 if trackDbObject['dataType'].lower() == 'bam':
59 subtools.add_track_json(self.trackList, trackDbObject['options']) 61 subtools.add_track_json(self.trackList, trackDbObject['options'])
60 elif trackDbObject['dataType'].lower() == 'bigwig': 62 elif trackDbObject['dataType'].lower() == 'bigwig':
61 subtools.add_track_json(self.trackList, trackDbObject['options']) 63 subtools.add_track_json(self.trackList, trackDbObject['options'])
62 else: 64 else:
102 104
103 def _prepareRefseq(self): 105 def _prepareRefseq(self):
104 subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath) 106 subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)
105 107
106 def _indexName(self): 108 def _indexName(self):
107 subtools.generate_names(self.mySpecieFolderPath) 109 subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList)
108 print "finished name index \n" 110 print "finished name index \n"
109 111
110 def _outHtml(self): 112 def _outHtml(self):
111 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')], 113 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
112 output_encoding='utf-8', encoding_errors='replace') 114 output_encoding='utf-8', encoding_errors='replace')