Mercurial > repos > yating-l > jbrowsearchivecreator

annotate tracks/HTMLFeatures.py @ 9:7cb67cbbd8e5 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 753ca09582fe0148e538103f2c211f7caa182966
author yating-l
date Tue, 01 May 2018 23:01:06 -0400
parents 237707a6b74d
children 3f9971a91096
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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
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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2 import json
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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3 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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5 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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6 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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7 from util import santitizer
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 HTMLFeatures(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(HTMLFeatures, 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):
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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15 """ set HTMLFeatures configuration options """
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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16 extraConfigs = dict()
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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17 self.extraSettings["clientConfig"] = dict()
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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18 self.extraSettings["config"] = dict()
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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19 if 'type' in self.extraSettings:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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20 extraConfigs["type"] = self.extraSettings['type']
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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21 if 'color' in self.extraSettings and self.extraSettings['color']:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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22 extraConfigs['feature_color'] = self.extraSettings['color']
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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23 else:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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24 extraConfigs['feature_color'] = "#000000"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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25 #self.extraSettings['clientConfig']['color'] = self.extraSettings['color']
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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26 if 'subfeatureClasses' in self.extraSettings:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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27 subfeature_css_class = santitizer.sanitize_name(self.trackLabel + "_" + self.extraSettings['subfeatureClasses'])
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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28 extraConfigs['subfeatureClasses'] = {self.extraSettings['subfeatureClasses']: subfeature_css_class}
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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30 if 'category' not in self.extraSettings or not self.extraSettings['category']:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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31 self.extraSettings['config']['category'] = "Default group"
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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32 else:
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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33 self.extraSettings['config']['category'] = self.extraSettings['category']
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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35 extraConfigs['config'] = json.dumps(self.extraSettings["config"])
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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36 extraConfigs['clientConfig'] = json.dumps(self.extraSettings["clientConfig"])
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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37 return extraConfigs
237707a6b74d planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
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