Mercurial > repos > yating-l > hubarchivecreator

comparison BedSimpleRepeats.py @ 52:c66803bff0cc draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
author yating-l
date Thu, 11 May 2017 17:21:15 -0400
parents 3e0c61b52a06
children b39dd0b5a166
comparison
equal deleted inserted replaced
51:364b8db8de17 52:c66803bff0cc
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 21 # TODO: Think about how to avoid repetition of the group_name everywhere
22 self.group_name = data_bed_simple_repeats["group_name"] 22 self.group_name = data_bed_simple_repeats["group_name"]
23 if data_bed_simple_repeats["long_label"]:
24 self.long_label = data_bed_simple_repeats["long_label"]
25 else:
26 self.long_label = self.name_bed_simple_repeats
23 27
24 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 28 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
25 29
26 # Sort processing 30 # Sort processing
27 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name) 31 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)
41 autoSql=auto_sql_option) 45 autoSql=auto_sql_option)
42 46
43 # Create the Track Object 47 # Create the Track Object
44 self.createTrack(file_path=trackName, 48 self.createTrack(file_path=trackName,
45 track_name=trackName, 49 track_name=trackName,
46 long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense', 50 long_label=self.long_label, track_type='bigBed 4 +', visibility='dense',
47 priority=self.priority, 51 priority=self.priority,
48 track_file=myBigBedFilePath, 52 track_file=myBigBedFilePath,
49 track_color=self.track_color, 53 track_color=self.track_color,
50 group_name=self.group_name) 54 group_name=self.group_name)
51 55