Mercurial > repos > yating-l > jbrowse_hub

comparison TrackHub.py @ 44:37422f705e9b draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty
author yating-l
date Mon, 20 Mar 2017 13:15:34 -0400
parents a5108e5010b4
children 15b4a74722d1
comparison
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43:b32f9f4793f8 44:37422f705e9b
105 bam_track = dict() 105 bam_track = dict()
106 bam_track['type'] = 'JBrowse/View/Track/Alignments2' 106 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
107 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM' 107 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
108 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName']) 108 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
109 bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index']) 109 bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index'])
110 bam_track.update(metadata) 110 bam_track['label'] = metadata['label']
111 bam_track['category'] = metadata['category']
111 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks') 112 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
112 113
113 def BigWig(self, track, metadata): 114 def BigWig(self, track, metadata):
114 #create trackList.json if not exist 115 #create trackList.json if not exist
115 self.createTrackList() 116 self.createTrackList()
118 #color_setting = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']} 119 #color_setting = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']}
119 #bigwig_track['style'] = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']} 120 #bigwig_track['style'] = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']}
120 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName']) 121 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
121 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot' 122 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
122 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig' 123 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
123 bigwig_track.update(metadata) 124 bigwig_track['label'] = metadata['label']
125 bigwig_track['style'] = metadata['style']
126 bigwig_track['category'] = metadata['category']
124 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks') 127 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
125 128
126 #If the metadata is not set, use the default value 129 #If the metadata is not set, use the default value
127 def SetMetadata(self, track, metadata): 130 def SetMetadata(self, track, metadata):
128 print metadata 131 print metadata