Mercurial > repos > yating-l > jbrowse_hub

comparison TrackHub.py @ 24:a051609fc8b4 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty
author yating-l
date Tue, 14 Mar 2017 17:03:13 -0400
parents 2a12d257f95d
children 55c62db02917
comparison
equal deleted inserted replaced
23:2a12d257f95d 24:a051609fc8b4
58 bam_track = dict() 58 bam_track = dict()
59 bam_track['type'] = 'JBrowse/View/Track/Alignments2' 59 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
60 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM' 60 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
61 bam_track['label'] = track['fileName'] 61 bam_track['label'] = track['fileName']
62 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName']) 62 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
63 bam_track['baiUrlTemplate'] = os.path.join('../raw', track['fileName'])
63 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks') 64 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
64 print "add bam track\n" 65 print "add bam track\n"
65 elif track['dataType'] == 'bigwig': 66 elif track['dataType'] == 'bigwig':
66 json_file = os.path.join(self.json, "trackList.json") 67 json_file = os.path.join(self.json, "trackList.json")
67 bigwig_track = dict() 68 bigwig_track = dict()
68 bigwig_track['label'] = track['fileName'] 69 bigwig_track['label'] = track['fileName']
69 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName']) 70 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
70 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot' 71 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
71 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig' 72 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
72 bigwig_track['variance_band'] = True
73 bigwig_track['style'] = dict()
74 bigwig_track['style']['pos_color'] = '#FFA600'
75 bigwig_track['style']['neg_color'] = '#005EFF'
76 bigwig_track['style']['clip_marker_color'] = 'red'
77 bigwig_track['style']['height'] = 100
78 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks') 73 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
79 else: 74 else:
80 gff3_file = os.path.join(self.raw, track['fileName']) 75 gff3_file = os.path.join(self.raw, track['fileName'])
81 label = track['fileName'] 76 label = track['fileName']
82 if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf': 77 if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf':