Mercurial > repos > rmarenco > hubarchivecreator

comparison Gtf.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
26 self.name_gtf = data_gtf["name"] 26 self.name_gtf = data_gtf["name"]
27 self.priority = data_gtf["order_index"] 27 self.priority = data_gtf["order_index"]
28 self.track_color = data_gtf["track_color"] 28 self.track_color = data_gtf["track_color"]
29 # TODO: Think about how to avoid repetition of the group_name everywhere 29 # TODO: Think about how to avoid repetition of the group_name everywhere
30 self.group_name = data_gtf["group_name"] 30 self.group_name = data_gtf["group_name"]
31 self.database = data_gtf["database"]
31 if data_gtf["long_label"]: 32 if data_gtf["long_label"]:
32 self.long_label = data_gtf["long_label"] 33 self.long_label = data_gtf["long_label"]
33 else: 34 else:
34 self.long_label = self.name_gtf 35 self.long_label = self.name_gtf
35 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf) 36 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
64 subtools.bedToBigBed(sorted_bigGenePred_file.name, 65 subtools.bedToBigBed(sorted_bigGenePred_file.name,
65 self.chromSizesFile.name, 66 self.chromSizesFile.name,
66 bigBedFile.name, 67 bigBedFile.name,
67 autoSql=auto_sql_option, 68 autoSql=auto_sql_option,
68 typeOption='bed12+8', 69 typeOption='bed12+8',
69 tab=True) 70 tab=True,
71 extraIndex='name')
70 72
71 73
72 # Create the Track Object 74 # Create the Track Object
73 self.createTrack(file_path=trackName, 75 self.createTrack(file_path=trackName,
74 track_name=trackName, 76 track_name=trackName,
75 long_label=self.long_label, track_type='bigGenePred', 77 long_label=self.long_label, track_type='bigGenePred',
76 visibility='dense', priority=self.priority, 78 visibility='dense', priority=self.priority,
77 track_file=myBigBedFilePath, 79 track_file=myBigBedFilePath,
78 track_color=self.track_color, 80 track_color=self.track_color,
79 group_name=self.group_name) 81 group_name=self.group_name,
82 database=self.database)
80 83
81 # TODO: Use Logging instead of print 84 # TODO: Use Logging instead of print
82 if modified_gtf.is_modified: 85 if modified_gtf.is_modified:
83 print("- Warning: Gtf %s created with a modified version of your Gtf because of start/end coordinates issues." 86 print("- Warning: Gtf %s created with a modified version of your Gtf because of start/end coordinates issues."
84 % self.name_gtf) 87 % self.name_gtf)