Mercurial > repos > rmarenco > hubarchivecreator

comparison BedSimpleRepeats.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
16 16
17 self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path 17 self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path
18 self.name_bed_simple_repeats = data_bed_simple_repeats["name"] 18 self.name_bed_simple_repeats = data_bed_simple_repeats["name"]
19 self.priority = data_bed_simple_repeats["order_index"] 19 self.priority = data_bed_simple_repeats["order_index"]
20 self.track_color = data_bed_simple_repeats["track_color"] 20 self.track_color = data_bed_simple_repeats["track_color"]
21 # TODO: Think about how to avoid repetition of the group_name everywhere
22 self.group_name = data_bed_simple_repeats["group_name"]
21 23
22 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 24 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
23 25
24 # Sort processing 26 # Sort processing
25 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name) 27 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)
42 self.createTrack(file_path=trackName, 44 self.createTrack(file_path=trackName,
43 track_name=trackName, 45 track_name=trackName,
44 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense', 46 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense',
45 priority=self.priority, 47 priority=self.priority,
46 track_file=myBigBedFilePath, 48 track_file=myBigBedFilePath,
47 track_color=self.track_color) 49 track_color=self.track_color,
50 group_name=self.group_name)
48 51
49 # dataURL = "tracks/%s" % trackName 52 # dataURL = "tracks/%s" % trackName
50 # 53 #
51 # trackDb = TrackDb( 54 # trackDb = TrackDb(
52 # trackName=trackName, 55 # trackName=trackName,