Mercurial > repos > rmarenco > hubarchivecreator

comparison BedSimpleRepeats.py @ 26:df42241d3731 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
author yating-l
date Mon, 03 Jul 2017 17:30:20 -0400
parents 2677f1899aa8
children
comparison
equal deleted inserted replaced
25:99dad5f9444c 26:df42241d3731
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 self.database = data_bed_simple_repeats["database"]
23 if data_bed_simple_repeats["long_label"]: 24 if data_bed_simple_repeats["long_label"]:
24 self.long_label = data_bed_simple_repeats["long_label"] 25 self.long_label = data_bed_simple_repeats["long_label"]
25 else: 26 else:
26 self.long_label = self.name_bed_simple_repeats 27 self.long_label = self.name_bed_simple_repeats
27 28
40 with open(myBigBedFilePath, 'w') as bigBedFile: 41 with open(myBigBedFilePath, 'w') as bigBedFile:
41 subtools.bedToBigBed(sortedBedFile.name, 42 subtools.bedToBigBed(sortedBedFile.name,
42 self.chromSizesFile.name, 43 self.chromSizesFile.name,
43 bigBedFile.name, 44 bigBedFile.name,
44 typeOption='bed4+12', 45 typeOption='bed4+12',
45 autoSql=auto_sql_option) 46 autoSql=auto_sql_option,
47 extraIndex='name'
48 )
46 49
47 # Create the Track Object 50 # Create the Track Object
48 self.createTrack(file_path=trackName, 51 self.createTrack(file_path=trackName,
49 track_name=trackName, 52 track_name=trackName,
50 long_label=self.long_label, track_type='bigBed 4 +', visibility='dense', 53 long_label=self.long_label, track_type='bigBed 4 +', visibility='dense',
51 priority=self.priority, 54 priority=self.priority,
52 track_file=myBigBedFilePath, 55 track_file=myBigBedFilePath,
53 track_color=self.track_color, 56 track_color=self.track_color,
54 group_name=self.group_name) 57 group_name=self.group_name,
58 database=self.database)
55 59
56 # dataURL = "tracks/%s" % trackName 60 # dataURL = "tracks/%s" % trackName
57 # 61 #
58 # trackDb = TrackDb( 62 # trackDb = TrackDb(
59 # trackName=trackName, 63 # trackName=trackName,