Mercurial > repos > rmarenco > hubarchivecreator

comparison Bed.py @ 17:c02720d1afee draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
author rmarenco
date Fri, 30 Sep 2016 15:14:24 -0400
parents 3233451a3bd6
children 2677f1899aa8
comparison
equal deleted inserted replaced
16:3233451a3bd6 17:c02720d1afee
22 22
23 self.data_bed_generic = data_bed_generic 23 self.data_bed_generic = data_bed_generic
24 self.name_bed_generic = self.data_bed_generic["name"] 24 self.name_bed_generic = self.data_bed_generic["name"]
25 self.priority = self.data_bed_generic["order_index"] 25 self.priority = self.data_bed_generic["order_index"]
26 self.track_color = self.data_bed_generic["track_color"] 26 self.track_color = self.data_bed_generic["track_color"]
27 # TODO: Think about how to avoid repetition of the group_name everywhere
28 self.group_name = self.data_bed_generic["group_name"]
29
27 30
28 # Sort processing 31 # Sort processing
29 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) 32 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
30 33
31 # bedToBigBed processing 34 # bedToBigBed processing
42 self.createTrack(file_path=trackName, 45 self.createTrack(file_path=trackName,
43 track_name=trackName, 46 track_name=trackName,
44 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense', 47 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
45 priority=self.priority, 48 priority=self.priority,
46 track_file=myBigBedFilePath, 49 track_file=myBigBedFilePath,
47 track_color=self.track_color) 50 track_color=self.track_color,
51 group_name=self.group_name)
48 52
49 # dataURL = "tracks/%s" % trackName 53 # dataURL = "tracks/%s" % trackName
50 # 54 #
51 # trackDb = TrackDb( 55 # trackDb = TrackDb(
52 # trackName=trackName, 56 # trackName=trackName,