Mercurial > repos > rmarenco > hubarchivecreator
diff Bam.py @ 11:d05236b15f81 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
author | rmarenco |
---|---|
date | Wed, 27 Jul 2016 10:10:49 -0400 |
parents | acc233161f50 |
children | 3233451a3bd6 |
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--- a/Bam.py Thu Jul 21 05:58:51 2016 -0400 +++ b/Bam.py Wed Jul 27 10:10:49 2016 -0400 @@ -24,11 +24,15 @@ self.data_bam = data_bam # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension - self.name_bam = self.data_bam["name"] + ".bam" + if ".bam" not in self.data_bam["name"]: + self.name_bam = self.data_bam["name"] + ".bam" + else: + self.name_bam = self.data_bam["name"] + self.priority = self.data_bam["order_index"] self.index_bam = self.data_bam["index"] - print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam) + #print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam) # First: Add the bam file # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html) @@ -42,23 +46,29 @@ shutil.copyfile(self.index_bam, bam_index_file_path) # Create the Track Object - dataURL = "tracks/%s" % self.name_bam + self.createTrack(file_path=self.name_bam, + track_name=self.name_bam, + long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority, + track_file=bam_index_file_path) + # + # dataURL = "tracks/%s" % self.name_bam + # + # trackDb = TrackDb( + # trackName=self.name_bam, + # longLabel=self.name_bam, + # shortLabel=self.getShortName( self.name_bam ), + # trackDataURL=dataURL, + # trackType='bam', + # visibility='pack', + # priority=self.priority, + # ) + # + # # Return the Bam Track Object + # self.track = Track( + # trackFile=bam_index_file_path, + # trackDb=trackDb, + # ) - trackDb = TrackDb( - trackName=self.name_bam, - longLabel=self.name_bam, - shortLabel=self.getShortName( self.name_bam ), - trackDataURL=dataURL, - trackType='bam', - visibility='pack', - priority=self.priority, - ) - - # Return the Bam Track Object - self.track = Track( - trackFile=bam_index_file_path, - trackDb=trackDb, - ) - - print("- %s created in %s" % (self.name_bam, bam_file_path)) - print("- %s created in %s" % (self.index_bam, bam_index_file_path)) + print("- Bam %s created" % self.name_bam) + #print("- %s created in %s" % (self.name_bam, bam_file_path)) + #print("- %s created in %s" % (self.index_bam, bam_index_file_path))