Mercurial > repos > rmarenco > hubarchivecreator

comparison Gtf.py @ 23:2677f1899aa8 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
author yating-l
date Tue, 09 May 2017 15:42:43 -0400
parents 0152500d9acd
children df42241d3731
comparison
equal deleted inserted replaced
22:7ddf651457df 23:2677f1899aa8
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 31 if data_gtf["long_label"]:
32 self.long_label = data_gtf["long_label"]
33 else:
34 self.long_label = self.name_gtf
32 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf) 35 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
33 36
34 # TODO: See if we need these temporary files as part of the generated files 37 # TODO: See if we need these temporary files as part of the generated files
35 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") 38 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
36 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred") 39 unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
67 70
68 71
69 # Create the Track Object 72 # Create the Track Object
70 self.createTrack(file_path=trackName, 73 self.createTrack(file_path=trackName,
71 track_name=trackName, 74 track_name=trackName,
72 long_label=self.name_gtf, track_type='bigGenePred', 75 long_label=self.long_label, track_type='bigGenePred',
73 visibility='dense', priority=self.priority, 76 visibility='dense', priority=self.priority,
74 track_file=myBigBedFilePath, 77 track_file=myBigBedFilePath,
75 track_color=self.track_color, 78 track_color=self.track_color,
76 group_name=self.group_name) 79 group_name=self.group_name)
77 80