Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tracks/CanvasFeatures.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 be34d213ec6a
children
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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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1 #!/usr/bin/env python
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2 import os
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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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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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10 class CanvasFeatures(TrackDb):
31a41ce128cc planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
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11 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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12 super(CanvasFeatures, 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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14 def prepareExtraSetting(self):
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15 if 'category' not in self.extraSettings or not self.extraSettings['category']:
d17f629f5486 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
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16 self.extraSettings['category'] = "Default group"
d17f629f5486 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
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17 self.extraSettings['style'] = {}
d17f629f5486 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
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18 self.extraSettings['style']['className'] = 'feature'
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19 if 'color' not in self.extraSettings or not self.extraSettings['color']:
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20 self.extraSettings['style']['color'] = "#FFA600"
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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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21 else:
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22 self.extraSettings['style']['color'] = self.extraSettings['color']
d17f629f5486 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
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23 track = dict()
d17f629f5486 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
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24 track['type'] = 'JBrowse/View/Track/' + self.trackType
d17f629f5486 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
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25 track['storeClass'] = 'JBrowse/Store/SeqFeature/GFF3Tabix'
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26 if self.dataType == 'gff':
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627cce51523f planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 2285eddcfe689d70d89571a045f204b74cc6890c-dirty
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27 # need .gff3.gz extension to index the name of the track with generate-name.pl
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28 track['urlTemplate'] = os.path.join('tracks', self.trackName + '.gff3.gz')
4a69515eed63 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 91271a6c0d39c923f0d460b2979247baa297286b-dirty
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29 else:
4a69515eed63 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 91271a6c0d39c923f0d460b2979247baa297286b-dirty
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30 track['urlTemplate'] = os.path.join('tracks', self.trackName)
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31 if 'glyph' in self.extraSettings:
061da5d3a219 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3160592f4119e684ab5843dd28a2e6cf11df0121-dirty
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32 track['glyph'] = self.extraSettings['glyph']
061da5d3a219 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3160592f4119e684ab5843dd28a2e6cf11df0121-dirty
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33 if 'subfeatureClasses' in self.extraSettings:
061da5d3a219 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3160592f4119e684ab5843dd28a2e6cf11df0121-dirty
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34 track['subfeatureClasses'] = self.extraSettings['subfeatureClasses']
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35 track['label'] = self.trackLabel
d17f629f5486 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
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36 track['category'] = self.extraSettings['category']
d17f629f5486 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
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37 track['style'] = self.extraSettings['style']
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be34d213ec6a planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
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38 if "menuTemplate" in self.extraSettings:
be34d213ec6a planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
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39 track["menuTemplate"] = [{}, self.extraSettings["menuTemplate"]]
be34d213ec6a planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
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40 #self.track["menuTemplate"] += [{"label" : "View details"}, {"label" : "Highlight this gene"}, self.extraSettings["menuTemplate"]]
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41 extraConfigs = track
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42 return extraConfigs
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