Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tracks/CanvasFeatures.py @ 18:79b23a8afb15 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 398c2fd8d1cb38decddf8cd58574cf39b1b52eaa
author yating-l
date Fri, 20 Jul 2018 12:25:36 -0400
parents 315a40b0b694
children 62dee5369e80
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237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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1 #!/usr/bin/env python
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2 import os
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237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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3 import json
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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4 import logging
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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6 from TrackDb import TrackDb
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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7 from util import subtools
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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10 class CanvasFeatures(TrackDb):
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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11 def __init__(self, trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings=None):
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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12 super(CanvasFeatures, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings)
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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14 def prepareExtraSetting(self):
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5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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15 if 'category' not in self.extraSettings or not self.extraSettings['category']:
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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16 self.extraSettings['category'] = "Default group"
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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17 self.extraSettings['style'] = {}
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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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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5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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20 self.extraSettings['style']['color'] = "#FFA600"
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237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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21 else:
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5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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22 self.extraSettings['style']['color'] = self.extraSettings['color']
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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23 track = dict()
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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24 track['type'] = 'JBrowse/View/Track/' + self.trackType
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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25 track['storeClass'] = 'JBrowse/Store/SeqFeature/GFF3Tabix'
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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26 if self.dataType == 'gff':
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56d9d10b4990 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 2285eddcfe689d70d89571a045f204b74cc6890c
yating-l
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27 # need .gff3.gz extension to index the name of the track with generate-name.pl
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5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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28 track['urlTemplate'] = os.path.join('tracks', self.trackName + '.gff3.gz')
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237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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29 else:
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5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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30 track['urlTemplate'] = os.path.join('tracks', self.trackName)
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8886033b4f84 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 4e8e5448a54f794bced67046e236988031616180
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31 if 'glyph' in self.extraSettings:
8886033b4f84 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 4e8e5448a54f794bced67046e236988031616180
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32 track['glyph'] = self.extraSettings['glyph']
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e2ebf58c9068 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 8ace9ad3a69a56a9b0d5feae266f90301d9aac77
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33 if 'subfeatureClasses' in self.extraSettings:
e2ebf58c9068 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 8ace9ad3a69a56a9b0d5feae266f90301d9aac77
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34 track['subfeatureClasses'] = self.extraSettings['subfeatureClasses']
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5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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35 track['label'] = self.trackLabel
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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36 track['category'] = self.extraSettings['category']
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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37 track['style'] = self.extraSettings['style']
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38 if "menuTemplate" in self.extraSettings:
3f9971a91096 planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
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39 track["menuTemplate"] = [{}, self.extraSettings["menuTemplate"]]
3f9971a91096 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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5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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41 extraConfigs = track
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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42 return extraConfigs
5d5fdcb798da planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
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