Mercurial > repos > yating-l > jbrowsearchivecreator
diff tracks/BigwigFeatures.py @ 6:237707a6b74d draft
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
author | yating-l |
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date | Thu, 15 Feb 2018 17:05:05 -0500 |
parents | |
children | 62dee5369e80 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tracks/BigwigFeatures.py Thu Feb 15 17:05:05 2018 -0500 @@ -0,0 +1,45 @@ +#!/usr/bin/env python +import os +import json +import logging + +from TrackDb import TrackDb +from util import subtools +from util import santitizer + + +class BigwigFeatures(TrackDb): + def __init__(self, trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings=None): + super(BigwigFeatures, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings) + + def prepareExtraSetting(self): + if 'category' not in self.extraSettings or not self.extraSettings['category']: + self.extraSettings['category'] = "Default group" + if 'color' not in self.extraSettings or not self.extraSettings['color']: + self.extraSettings['style'] = {} + self.extraSettings['style']['pos_color'] = "#FFA600" + else: + self.extraSettings['style'] = {} + self.extraSettings['style']['pos_color'] = self.extraSettings['color'] + + + ''' + if 'style' not in self.extraSettings: + self.extraSettings['style'] = {} + if 'pos_color' not in self.extraSettings['style'] or self.extraSettings['style']['pos_color'] == '': + self.extraSettings['style']['pos_color'] = "#FFA600" + if 'neg_color' not in self.extraSettings['style'] or self.extraSettings['style']['neg_color'] == '': + self.extraSettings['style']['neg_color'] = "#005EFF" + ''' + bigwig_track = dict() + bigwig_track['urlTemplate'] = os.path.join('bbi', self.trackName) + bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot' + bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig' + bigwig_track['label'] = self.trackLabel + bigwig_track['style'] = self.extraSettings['style'] + bigwig_track['category'] = self.extraSettings['category'] + #extraConfigs = json.dumps(bigwig_track) + extraConfigs = bigwig_track + return extraConfigs + + \ No newline at end of file