Mercurial > repos > yating-l > hubarchivecreator

comparison BedBlastAlignments.py @ 52:c66803bff0cc draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
author yating-l
date Thu, 11 May 2017 17:21:15 -0400
parents 364b8db8de17
children b39dd0b5a166
comparison
equal deleted inserted replaced
51:364b8db8de17 52:c66803bff0cc
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 24 if data_bed_blast_alignments["long_label"]:
25 self.long_label = data_bed_blast_alignments["long_label"]
26 else:
27 self.long_label = self.name_bed_blast_alignments
25 #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 28 #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
26 29
27 # Sort processing 30 # Sort processing
28 #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name) 31 #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name)
29 32
43 tab='True', 46 tab='True',
44 autoSql=auto_sql_option) 47 autoSql=auto_sql_option)
45 48
46 self.createTrack(file_path=trackName, 49 self.createTrack(file_path=trackName,
47 track_name=trackName, 50 track_name=trackName,
48 long_label=self.name_bed_blast_alignments, track_type='bigBed 12 +', visibility='dense', 51 long_label=self.long_label, track_type='bigBed 12 +', visibility='dense',
49 priority=self.priority, 52 priority=self.priority,
50 track_file=myBigBedFilePath, 53 track_file=myBigBedFilePath,
51 track_color=self.track_color, 54 track_color=self.track_color,
52 group_name=self.group_name) 55 group_name=self.group_name)
53 56