Mercurial > repos > rmarenco > hubarchivecreator

comparison Psl.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
17 self.name_psl = data_psl["name"] 17 self.name_psl = data_psl["name"]
18 self.priority = data_psl["order_index"] 18 self.priority = data_psl["order_index"]
19 self.track_color = data_psl["track_color"] 19 self.track_color = data_psl["track_color"]
20 # TODO: Think about how to avoid repetition of the group_name everywhere 20 # TODO: Think about how to avoid repetition of the group_name everywhere
21 self.group_name = data_psl["group_name"] 21 self.group_name = data_psl["group_name"]
22 self.database = data_psl["database"]
22 if data_psl["long_label"]: 23 if data_psl["long_label"]:
23 self.long_label = data_psl["long_label"] 24 self.long_label = data_psl["long_label"]
24 else: 25 else:
25 self.long_label = self.name_psl 26 self.long_label = self.name_psl
26 # Temporary files 27 # Temporary files
46 subtools.bedToBigBed(sorted_bed_formatted_psl_file.name, 47 subtools.bedToBigBed(sorted_bed_formatted_psl_file.name,
47 self.chromSizesFile.name, 48 self.chromSizesFile.name,
48 big_psl_file.name, 49 big_psl_file.name,
49 autoSql=auto_sql_option, 50 autoSql=auto_sql_option,
50 typeOption='bed12+12', 51 typeOption='bed12+12',
51 tab=True) 52 tab=True,
53 extraIndex='name')
52 54
53 # Create the Track Object 55 # Create the Track Object
54 self.createTrack(file_path=trackName, 56 self.createTrack(file_path=trackName,
55 track_name=trackName, 57 track_name=trackName,
56 long_label=self.long_label, 58 long_label=self.long_label,
57 track_type='bigPsl', visibility='dense', 59 track_type='bigPsl', visibility='dense',
58 priority=self.priority, 60 priority=self.priority,
59 track_file=my_big_psl_file_path, 61 track_file=my_big_psl_file_path,
60 track_color=self.track_color, 62 track_color=self.track_color,
61 group_name=self.group_name) 63 group_name=self.group_name,
64 database=self.database)
62 65
63 print("- BigPsl %s created" % self.name_psl) 66 print("- BigPsl %s created" % self.name_psl)