Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tracks/CanvasFeatures.py @ 38:d17f629f5486 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty
author yating-l
date Fri, 06 Apr 2018 13:44:56 -0400
parents 31a41ce128cc
children 4a69515eed63
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1 #!/usr/bin/env python
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2 import os
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3 import json
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4 import logging
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6 from TrackDb import TrackDb
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7 from util import subtools
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10 class CanvasFeatures(TrackDb):
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11 def __init__(self, trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings=None):
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12 super(CanvasFeatures, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings)
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14 def prepareExtraSetting(self):
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15 if 'category' not in self.extraSettings or not self.extraSettings['category']:
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16 self.extraSettings['category'] = "Default group"
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17 self.extraSettings['style'] = {}
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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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21 else:
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22 self.extraSettings['style']['color'] = self.extraSettings['color']
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23 track = dict()
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24 track['type'] = 'JBrowse/View/Track/' + self.trackType
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25 track['storeClass'] = 'JBrowse/Store/SeqFeature/GFF3Tabix'
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26 track['urlTemplate'] = os.path.join('tracks', self.trackName)
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27 track['label'] = self.trackLabel
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28 track['category'] = self.extraSettings['category']
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29 track['style'] = self.extraSettings['style']
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30 extraConfigs = track
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31 return extraConfigs
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33 # def prepareExtraSetting(self):
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34 # """ set CanvasFeatures configuration options """
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35 # extraConfigs = dict()
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36 # self.extraSettings["clientConfig"] = dict()
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37 # self.extraSettings["config"] = dict()
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38 # if 'color' not in self.extraSettings or not self.extraSettings['color']:
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39 # self.extraSettings["clientConfig"]['color'] = "#daa520"
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40 # else:
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41 # self.extraSettings["clientConfig"]['color'] = self.extraSettings['color']
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42 # if 'category' not in self.extraSettings or not self.extraSettings['category']:
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43 # self.extraSettings["config"]['category'] = "Default group"
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44 # else:
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45 # self.extraSettings["config"]['category'] = self.extraSettings['category']
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46 # if 'glyph' in self.extraSettings:
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47 # self.extraSettings["config"]['glyph'] = self.extraSettings['glyph']
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48 # if 'transcriptType' in self.extraSettings:
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49 # self.extraSettings['config']['transcriptType'] = self.extraSettings['transcriptType']
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50 # extraConfigs["config"] = json.dumps(self.extraSettings["config"])
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51 # extraConfigs["clientConfig"] = json.dumps(self.extraSettings["clientConfig"])
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52 # return extraConfigs