Mercurial > repos > rmarenco > hubarchivecreator
diff BigWig.py @ 24:fcc1021bd496 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
author | yating-l |
---|---|
date | Wed, 31 May 2017 11:35:16 -0400 |
parents | 2677f1899aa8 |
children | df42241d3731 |
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--- a/BigWig.py Tue May 09 15:42:43 2017 -0400 +++ b/BigWig.py Wed May 31 11:35:16 2017 -0400 @@ -2,6 +2,8 @@ import os import shutil +from subprocess import Popen, PIPE +import re # Internal dependencies from Datatype import Datatype @@ -36,30 +38,37 @@ self.createTrack(file_path=trackName, track_name=trackName, long_label=self.long_label, - track_type='bigWig', visibility='full', + track_type=self.determine_track_type(myBigWigFilePath), + visibility='full', priority=self.priority, track_file=myBigWigFilePath, track_color=self.track_color, group_name=self.group_name) - # dataURL = "tracks/%s" % trackName - # - # # Return the BigBed track - # - # trackDb = TrackDb( - # trackName=trackName, - # longLabel=self.name_bigwig, - # shortLabel=self.getShortName( self.name_bigwig ), - # trackDataURL=dataURL, - # trackType='bigWig', - # visibility='full', - # priority=self.priority, - # ) - # - # self.track = Track( - # trackFile=myBigWigFilePath, - # trackDb=trackDb, - # ) - print("- BigWig %s created" % self.name_bigwig) #print("- %s created in %s" % (trackName, myBigWigFilePath)) + + def determine_track_type(self, bw_file): + """ + bigWig tracks must declare the expected signal range for the data + (See https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html). + This method determines the range of values for a bigWig file using + the bigWigInfo program. + + Implementation of reading from stdout is based on a Stackoverflow post: + http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate + + :param bw_file: path to a bigWig file + + :returns: the bigWig track type + """ + cmd_ph = Popen(["bigWigInfo", "-minMax", bw_file], + stdout=PIPE, bufsize=1) + + with cmd_ph.stdout: + for line in iter(cmd_ph.stdout.readline, b''): + bw_type = "bigWig %s" % line.rstrip() + + cmd_ph.wait() + + return bw_type