Mercurial > repos > yating-l > jbrowse_hub
comparison TrackHub.py @ 26:a4a54b925c73 draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty
| author | yating-l |
|---|---|
| date | Wed, 15 Mar 2017 10:51:23 -0400 |
| parents | 55c62db02917 |
| children | d8049deb0c97 |
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| 25:55c62db02917 | 26:a4a54b925c73 |
|---|---|
| 52 except OSError as e: | 52 except OSError as e: |
| 53 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror) | 53 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror) |
| 54 #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings | 54 #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings |
| 55 def addTrack(self, track): | 55 def addTrack(self, track): |
| 56 if track['dataType'] == 'bam': | 56 if track['dataType'] == 'bam': |
| 57 self.createTrackList() | |
| 57 json_file = os.path.join(self.json, "trackList.json") | 58 json_file = os.path.join(self.json, "trackList.json") |
| 58 bam_track = dict() | 59 bam_track = dict() |
| 59 bam_track['type'] = 'JBrowse/View/Track/Alignments2' | 60 bam_track['type'] = 'JBrowse/View/Track/Alignments2' |
| 60 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM' | 61 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM' |
| 61 bam_track['label'] = track['fileName'] | 62 bam_track['label'] = track['fileName'] |
| 62 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName']) | 63 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName']) |
| 63 #bam_track['baiUrlTemplate'] = os.path.join('../raw', track['fileName']) | 64 bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index']) |
| 64 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks') | 65 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks') |
| 65 print "add bam track\n" | 66 print "add bam track\n" |
| 66 elif track['dataType'] == 'bigwig': | 67 elif track['dataType'] == 'bigwig': |
| 68 self.createTrackList() | |
| 67 json_file = os.path.join(self.json, "trackList.json") | 69 json_file = os.path.join(self.json, "trackList.json") |
| 68 bigwig_track = dict() | 70 bigwig_track = dict() |
| 69 bigwig_track['label'] = track['fileName'] | 71 bigwig_track['label'] = track['fileName'] |
| 70 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName']) | 72 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName']) |
| 71 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot' | 73 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot' |
| 111 htmlstr += zipfiles % relative_file_path | 113 htmlstr += zipfiles % relative_file_path |
| 112 | 114 |
| 113 #htmlstr = htmlstr % zipfile | 115 #htmlstr = htmlstr % zipfile |
| 114 htmlfile.write(htmlstr) | 116 htmlfile.write(htmlstr) |
| 115 | 117 |
| 118 def createTrackList(self): | |
| 119 trackList = os.path.join(self.json, "trackList.json") | |
| 120 if not os.path.exists(trackList): | |
| 121 os.mknod(trackList) | |
| 122 #open(trackList,'w').close() | |
| 123 | |
| 124 | |
| 116 | 125 |
| 117 | 126 |
| 118 | 127 |
| 119 | 128 |