Mercurial > repos > yating-l > jbrowsearchivecreator
diff tracks/CanvasFeatures.py @ 7:5d5fdcb798da draft
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
author | yating-l |
---|---|
date | Fri, 20 Apr 2018 13:51:23 -0400 |
parents | 237707a6b74d |
children | 56d9d10b4990 |
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--- a/tracks/CanvasFeatures.py Thu Feb 15 17:05:05 2018 -0500 +++ b/tracks/CanvasFeatures.py Fri Apr 20 13:51:23 2018 -0400 @@ -1,4 +1,5 @@ #!/usr/bin/env python +import os import json import logging @@ -11,22 +12,24 @@ super(CanvasFeatures, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings) def prepareExtraSetting(self): - """ set CanvasFeatures configuration options """ - extraConfigs = dict() - self.extraSettings["clientConfig"] = dict() - self.extraSettings["config"] = dict() + if 'category' not in self.extraSettings or not self.extraSettings['category']: + self.extraSettings['category'] = "Default group" + self.extraSettings['style'] = {} + self.extraSettings['style']['className'] = 'feature' if 'color' not in self.extraSettings or not self.extraSettings['color']: - self.extraSettings["clientConfig"]['color'] = "#daa520" + self.extraSettings['style']['color'] = "#FFA600" else: - self.extraSettings["clientConfig"]['color'] = self.extraSettings['color'] - if 'category' not in self.extraSettings or not self.extraSettings['category']: - self.extraSettings["config"]['category'] = "Default group" + self.extraSettings['style']['color'] = self.extraSettings['color'] + track = dict() + track['type'] = 'JBrowse/View/Track/' + self.trackType + track['storeClass'] = 'JBrowse/Store/SeqFeature/GFF3Tabix' + if self.dataType == 'gff': + track['urlTemplate'] = os.path.join('tracks', self.trackName + '.gff3.gz') else: - self.extraSettings["config"]['category'] = self.extraSettings['category'] - if 'glyph' in self.extraSettings: - self.extraSettings["config"]['glyph'] = self.extraSettings['glyph'] - if 'transcriptType' in self.extraSettings: - self.extraSettings['config']['transcriptType'] = self.extraSettings['transcriptType'] - extraConfigs["config"] = json.dumps(self.extraSettings["config"]) - extraConfigs["clientConfig"] = json.dumps(self.extraSettings["clientConfig"]) - return extraConfigs \ No newline at end of file + track['urlTemplate'] = os.path.join('tracks', self.trackName) + track['label'] = self.trackLabel + track['category'] = self.extraSettings['category'] + track['style'] = self.extraSettings['style'] + extraConfigs = track + return extraConfigs +