Mercurial > repos > rmarenco > hubarchivecreator

comparison Gff3.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
20 self.name_gff3 = data_gff3["name"] 20 self.name_gff3 = data_gff3["name"]
21 self.priority = data_gff3["order_index"] 21 self.priority = data_gff3["order_index"]
22 self.track_color = data_gff3["track_color"] 22 self.track_color = data_gff3["track_color"]
23 # TODO: Think about how to avoid repetition of the group_name everywhere 23 # TODO: Think about how to avoid repetition of the group_name everywhere
24 self.group_name = data_gff3["group_name"] 24 self.group_name = data_gff3["group_name"]
25 self.database = data_gff3["database"]
25 if data_gff3["long_label"]: 26 if data_gff3["long_label"]:
26 self.long_label = data_gff3["long_label"] 27 self.long_label = data_gff3["long_label"]
27 else: 28 else:
28 self.long_label = self.name_gff3 29 self.long_label = self.name_gff3
29 # TODO: See if we need these temporary files as part of the generated files 30 # TODO: See if we need these temporary files as part of the generated files
53 subtools.bedToBigBed(sorted_biGenePred_file.name, 54 subtools.bedToBigBed(sorted_biGenePred_file.name,
54 self.chromSizesFile.name, 55 self.chromSizesFile.name,
55 bigBedFile.name, 56 bigBedFile.name,
56 autoSql=auto_sql_option, 57 autoSql=auto_sql_option,
57 typeOption='bed12+8', 58 typeOption='bed12+8',
58 tab=True) 59 tab=True,
60 extraIndex='name')
59 61
60 # Create the Track Object 62 # Create the Track Object
61 self.createTrack(file_path=trackName, 63 self.createTrack(file_path=trackName,
62 track_name=trackName, 64 track_name=trackName,
63 long_label=self.long_label, 65 long_label=self.long_label,
64 track_type='bigGenePred', visibility='dense', 66 track_type='bigGenePred', visibility='dense',
65 priority=self.priority, 67 priority=self.priority,
66 track_file=myBigBedFilePath, 68 track_file=myBigBedFilePath,
67 track_color=self.track_color, 69 track_color=self.track_color,
68 group_name=self.group_name) 70 group_name=self.group_name,
71 database=self.database)
69 72
70 print("- Gff3 %s created" % self.name_gff3) 73 print("- Gff3 %s created" % self.name_gff3)