Mercurial > repos > yating-l > jbrowsearchivecreator
view tracks/BamFeatures.py @ 7:5d5fdcb798da draft
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
author | yating-l |
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date | Fri, 20 Apr 2018 13:51:23 -0400 |
parents | 237707a6b74d |
children | 62dee5369e80 |
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#!/usr/bin/env python import os import json import logging from TrackDb import TrackDb from util import subtools from util import santitizer class BamFeatures(TrackDb): def __init__(self, trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings=None): super(BamFeatures, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings) def prepareExtraSetting(self): if 'category' not in self.extraSettings or not self.extraSettings['category']: self.extraSettings['category'] = "Default group" bam_track = dict() bam_track['type'] = 'JBrowse/View/Track/Alignments2' bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM' bam_track['urlTemplate'] = os.path.join('bbi', self.trackName) bam_track['baiUrlTemplate'] = os.path.join('bbi', self.extraSettings['index']) bam_track['label'] = self.trackLabel bam_track['category'] = self.extraSettings['category'] #extraConfigs = json.dumps(bam_track) extraConfigs = bam_track return extraConfigs