Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tracks/BigwigFeatures.py @ 50:804e7217f27c draft default tip

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3afab1eb0da4823419945c523a1d37cd5973e7f6-dirty
author yating-l
date Fri, 20 Jul 2018 11:38:01 -0400
parents 31a41ce128cc
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
yating-l
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1 #!/usr/bin/env python
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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2 import os
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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3 import json
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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4 import logging
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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6 from TrackDb import TrackDb
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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7 from util import subtools
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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8 from util import santitizer
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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11 class BigwigFeatures(TrackDb):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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12 def __init__(self, trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings=None):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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13 super(BigwigFeatures, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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15 def prepareExtraSetting(self):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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16 if 'category' not in self.extraSettings or not self.extraSettings['category']:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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17 self.extraSettings['category'] = "Default group"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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18 if 'color' not in self.extraSettings or not self.extraSettings['color']:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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19 self.extraSettings['style'] = {}
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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20 self.extraSettings['style']['pos_color'] = "#FFA600"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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21 else:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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22 self.extraSettings['style'] = {}
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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23 self.extraSettings['style']['pos_color'] = self.extraSettings['color']
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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26 '''
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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27 if 'style' not in self.extraSettings:
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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28 self.extraSettings['style'] = {}
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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29 if 'pos_color' not in self.extraSettings['style'] or self.extraSettings['style']['pos_color'] == '':
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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30 self.extraSettings['style']['pos_color'] = "#FFA600"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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31 if 'neg_color' not in self.extraSettings['style'] or self.extraSettings['style']['neg_color'] == '':
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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32 self.extraSettings['style']['neg_color'] = "#005EFF"
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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33 '''
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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34 bigwig_track = dict()
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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35 bigwig_track['urlTemplate'] = os.path.join('bbi', self.trackName)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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36 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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37 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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38 bigwig_track['label'] = self.trackLabel
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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39 bigwig_track['style'] = self.extraSettings['style']
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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40 bigwig_track['category'] = self.extraSettings['category']
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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41 #extraConfigs = json.dumps(bigwig_track)
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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42 extraConfigs = bigwig_track
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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43 return extraConfigs
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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