Mercurial > repos > yating-l > jbrowse_hub

comparison TrackHub.py @ 48:6803152ea92a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 073c8ceda5eddfb4ccd07cfa96a8353e5535ffaf-dirty
author yating-l
date Tue, 28 Mar 2017 18:13:27 -0400
parents 15b4a74722d1
children 193e94a43f0f
comparison
equal deleted inserted replaced
47:b7bf45272ab7 48:6803152ea92a
114 def BigWig(self, track, metadata): 114 def BigWig(self, track, metadata):
115 #create trackList.json if not exist 115 #create trackList.json if not exist
116 self.createTrackList() 116 self.createTrackList()
117 json_file = os.path.join(self.json, "trackList.json") 117 json_file = os.path.join(self.json, "trackList.json")
118 bigwig_track = dict() 118 bigwig_track = dict()
119 #color_setting = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']}
120 #bigwig_track['style'] = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']}
121 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName']) 119 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
122 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot' 120 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
123 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig' 121 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
124 bigwig_track['label'] = metadata['label'] 122 bigwig_track['label'] = metadata['label']
125 bigwig_track['style'] = metadata['style'] 123 bigwig_track['style'] = metadata['style']
126 bigwig_track['category'] = metadata['category'] 124 bigwig_track['category'] = metadata['category']
127 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks') 125 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
128 126
129 #If the metadata is not set, use the default value 127 #If the metadata is not set, use the default value
130 def SetMetadata(self, track, metadata): 128 def SetMetadata(self, track, metadata):
131 #print metadata
132 #track.update(metadata)
133 if 'label' not in metadata.keys() or metadata['label'] == '': 129 if 'label' not in metadata.keys() or metadata['label'] == '':
134 metadata['label'] = track['fileName'] 130 metadata['label'] = track['fileName']
135 if 'color' not in metadata.keys() or metadata['color'] == '': 131 if 'color' not in metadata.keys() or metadata['color'] == '':
136 metadata['color'] = "#daa520" 132 metadata['color'] = "#daa520"
137 if track['dataType'] == 'bigwig': 133 if track['dataType'] == 'bigwig':