Mercurial > repos > rmarenco > hubarchivecreator

comparison BedBlastAlignments.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
19 self.name_bed_blast_alignments = data_bed_blast_alignments["name"] 19 self.name_bed_blast_alignments = data_bed_blast_alignments["name"]
20 self.priority = data_bed_blast_alignments["order_index"] 20 self.priority = data_bed_blast_alignments["order_index"]
21 self.track_color = data_bed_blast_alignments["track_color"] 21 self.track_color = data_bed_blast_alignments["track_color"]
22 # TODO: Think about how to avoid repetition of the group_name everywhere 22 # TODO: Think about how to avoid repetition of the group_name everywhere
23 self.group_name = data_bed_blast_alignments["group_name"] 23 self.group_name = data_bed_blast_alignments["group_name"]
24 self.database = data_bed_blast_alignments["database"]
24 if data_bed_blast_alignments["long_label"]: 25 if data_bed_blast_alignments["long_label"]:
25 self.long_label = data_bed_blast_alignments["long_label"] 26 self.long_label = data_bed_blast_alignments["long_label"]
26 else: 27 else:
27 self.long_label = self.name_bed_blast_alignments 28 self.long_label = self.name_bed_blast_alignments
28 #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 29 #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
42 subtools.bedToBigBed(self.input_bed_blast_alignments_false_path, 43 subtools.bedToBigBed(self.input_bed_blast_alignments_false_path,
43 self.chromSizesFile.name, 44 self.chromSizesFile.name,
44 bigBedFile.name, 45 bigBedFile.name,
45 typeOption='bed12+12', 46 typeOption='bed12+12',
46 tab='True', 47 tab='True',
47 autoSql=auto_sql_option) 48 autoSql=auto_sql_option,
49 extraIndex='name')
48 50
49 self.createTrack(file_path=trackName, 51 self.createTrack(file_path=trackName,
50 track_name=trackName, 52 track_name=trackName,
51 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense', 53 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense',
52 priority=self.priority, 54 priority=self.priority,
53 track_file=myBigBedFilePath, 55 track_file=myBigBedFilePath,
54 track_color=self.track_color, 56 track_color=self.track_color,
55 group_name=self.group_name) 57 group_name=self.group_name,
58 database=self.database
59 )
56 60
57 61
58 # dataURL = "tracks/%s" % trackName 62 # dataURL = "tracks/%s" % trackName
59 # 63 #
60 # trackDb = TrackDb( 64 # trackDb = TrackDb(