Mercurial > repos > rmarenco > hubarchivecreator
view BigWig.py @ 26:df42241d3731 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
author | yating-l |
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date | Mon, 03 Jul 2017 17:30:20 -0400 |
parents | fcc1021bd496 |
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#!/usr/bin/python import os import shutil from subprocess import Popen, PIPE import re # Internal dependencies from Datatype import Datatype from Track import Track from TrackDb import TrackDb class BigWig( Datatype ): def __init__(self, input_bigwig_path, data_bigwig): super(BigWig, self).__init__() self.track = None self.input_bigwig_path = input_bigwig_path self.name_bigwig = data_bigwig["name"] self.priority = data_bigwig["order_index"] self.track_color = data_bigwig["track_color"] # TODO: Think about how to avoid repetition of the group_name everywhere self.group_name = data_bigwig["group_name"] self.database = data_bigwig["database"] if data_bigwig["long_label"]: self.long_label = data_bigwig["long_label"] else: self.long_label = self.name_bigwig #print "Creating TrackHub BigWig from (falsePath: %s; name: %s)" % ( self.input_bigwig_path, self.name_bigwig ) trackName = "".join( ( self.name_bigwig, ".bigwig" ) ) myBigWigFilePath = os.path.join(self.myTrackFolderPath, trackName) shutil.copy(self.input_bigwig_path, myBigWigFilePath) # Create the Track Object self.createTrack(file_path=trackName, track_name=trackName, long_label=self.long_label, 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, database = self.database) 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