Mercurial > repos > yating-l > jbrowse_hub

comparison trackObject.py @ 39:75edbc203532 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
author yating-l
date Fri, 17 Mar 2017 19:00:01 -0400
parents 046c5bfc0413
children 4af741177682
comparison
equal deleted inserted replaced
38:3a3591cf27f9 39:75edbc203532
58 blastxmlToGff3.blastxml2gff3(dataFile, des_path) 58 blastxmlToGff3.blastxml2gff3(dataFile, des_path)
59 elif dataType == 'gtf': 59 elif dataType == 'gtf':
60 utils.gtfToGff3(dataFile, des_path, self.chrom_size) 60 utils.gtfToGff3(dataFile, des_path, self.chrom_size)
61 track['fileName'] = fileName 61 track['fileName'] = fileName
62 track['dataType'] = dataType 62 track['dataType'] = dataType
63 self.SetMetadata(track, metaData)
64 self.tracks.append(track)
65
66 #If the metadata is not set, use the default value
67 def SetMetadata(self, track, metaData):
63 track.update(metaData) 68 track.update(metaData)
64 #If the metadata is not set, use the default value
65 if 'name' not in metaData.keys() or track['name'] == '': 69 if 'name' not in metaData.keys() or track['name'] == '':
66 track['name'] = fileName 70 track['name'] = track['fileName']
67 if 'label' not in metaData.keys() or track['label'] == '': 71 if 'label' not in metaData.keys() or track['label'] == '':
68 track['label'] = track['name'] 72 track['label'] = track['name']
69 if 'track_color' not in metaData.keys() or track['track_color'] == '': 73 if 'track_color' not in metaData.keys() or track['track_color'] == '':
70 track['track_color'] = "#daa520" 74 track['track_color'] = "#daa520"
71 if 'track_type' not in metaData.keys() or track['track_type'] == '': 75 if 'track_type' not in metaData.keys() or track['track_type'] == '':
72 track['track_type'] = "CanvasFeatures" 76 track['track_type'] = "CanvasFeatures"
73 self.tracks.append(track) 77 if track['dataType'] == 'bigwig':
78 if 'pos_color' not in metaData.keys() or track['pos_color'] == '':
79 track['pos_color'] = "#FFA600"
80 if 'neg_color' not in metaData.keys() or track['neg_color'] == '':
81 track['neg_color'] = "#005EFF"