Mercurial > repos > rmarenco > hubarchivecreator

comparison BedSimpleRepeats.py @ 16:3233451a3bd6 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
author rmarenco
date Sun, 25 Sep 2016 11:25:38 -0400
parents 25809f699cb3
children c02720d1afee
comparison
equal deleted inserted replaced
15:2a45cd656e8e 16:3233451a3bd6
15 super(BedSimpleRepeats, self).__init__() 15 super(BedSimpleRepeats, self).__init__()
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 21
21 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 22 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
22 23
23 # Sort processing 24 # Sort processing
24 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name) 25 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)
40 # Create the Track Object 41 # Create the Track Object
41 self.createTrack(file_path=trackName, 42 self.createTrack(file_path=trackName,
42 track_name=trackName, 43 track_name=trackName,
43 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense', 44 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense',
44 priority=self.priority, 45 priority=self.priority,
45 track_file=myBigBedFilePath) 46 track_file=myBigBedFilePath,
47 track_color=self.track_color)
46 48
47 # dataURL = "tracks/%s" % trackName 49 # dataURL = "tracks/%s" % trackName
48 # 50 #
49 # trackDb = TrackDb( 51 # trackDb = TrackDb(
50 # trackName=trackName, 52 # trackName=trackName,