Mercurial > repos > yating-l > hubarchivecreator

comparison Bed.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 3f7c40fb51e8
children b39dd0b5a166
comparison
equal deleted inserted replaced
51:364b8db8de17 52:c66803bff0cc
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 27 # TODO: Think about how to avoid repetition of the group_name everywhere
28 self.group_name = self.data_bed_generic["group_name"] 28 self.group_name = self.data_bed_generic["group_name"]
29 29 if self.data_bed_generic["long_label"]:
30 self.long_label = self.data_bed_generic["long_label"]
31 else:
32 self.long_label = self.name_bed_generic
30 33
31 # Sort processing 34 # Sort processing
32 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) 35 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
33 36
34 # bedToBigBed processing 37 # bedToBigBed processing
42 self.bigBedFile.name) 45 self.bigBedFile.name)
43 46
44 # Create the Track Object 47 # Create the Track Object
45 self.createTrack(file_path=trackName, 48 self.createTrack(file_path=trackName,
46 track_name=trackName, 49 track_name=trackName,
47 long_label=self.name_bed_generic, track_type='bigBed', visibility='dense', 50 long_label=self.long_label, track_type='bigBed', visibility='dense',
48 priority=self.priority, 51 priority=self.priority,
49 track_file=myBigBedFilePath, 52 track_file=myBigBedFilePath,
50 track_color=self.track_color, 53 track_color=self.track_color,
51 group_name=self.group_name) 54 group_name=self.group_name)
52 55