Mercurial > repos > rmarenco > hubarchivecreator

comparison Gtf.py @ 17:c02720d1afee draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
author rmarenco
date Fri, 30 Sep 2016 15:14:24 -0400
parents 3233451a3bd6
children 0152500d9acd
comparison
equal deleted inserted replaced
16:3233451a3bd6 17:c02720d1afee
19 19
20 self.input_gtf_false_path = input_gtf_false_path 20 self.input_gtf_false_path = input_gtf_false_path
21 self.name_gtf = data_gtf["name"] 21 self.name_gtf = data_gtf["name"]
22 self.priority = data_gtf["order_index"] 22 self.priority = data_gtf["order_index"]
23 self.track_color = data_gtf["track_color"] 23 self.track_color = data_gtf["track_color"]
24 # TODO: Think about how to avoid repetition of the group_name everywhere
25 self.group_name = data_gtf["group_name"]
24 26
25 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf) 27 #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
26 28
27 # TODO: See if we need these temporary files as part of the generated files 29 # TODO: See if we need these temporary files as part of the generated files
28 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred") 30 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
59 self.createTrack(file_path=trackName, 61 self.createTrack(file_path=trackName,
60 track_name=trackName, 62 track_name=trackName,
61 long_label=self.name_gtf, track_type='bigGenePred', 63 long_label=self.name_gtf, track_type='bigGenePred',
62 visibility='dense', priority=self.priority, 64 visibility='dense', priority=self.priority,
63 track_file=myBigBedFilePath, 65 track_file=myBigBedFilePath,
64 track_color=self.track_color) 66 track_color=self.track_color,
67 group_name=self.group_name)
65 68
66 print("- Gtf %s created" % self.name_gtf) 69 print("- Gtf %s created" % self.name_gtf)