view Gtf.py @ 11:d05236b15f81 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2

#!/usr/bin/python

import os
import tempfile

# Internal dependencies
from Datatype import Datatype
from Track import Track
from TrackDb import TrackDb
from util import subtools


class Gtf( Datatype ):
    def __init__( self, input_gtf_false_path, data_gtf):

        super(Gtf, self).__init__()

        self.track = None

        self.input_gtf_false_path = input_gtf_false_path
        self.name_gtf = data_gtf["name"]
        self.priority = data_gtf["order_index"]

        #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)

        # TODO: See if we need these temporary files as part of the generated files
        genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
        unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")

        # GtfToGenePred
        subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name)

        # TODO: From there, refactor because common use with Gff3.py
        #  genePredToBed processing
        subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)

        # Sort processing
        subtools.sort(unsortedBedFile.name, sortedBedFile.name)

        # bedToBigBed processing
        # TODO: Change the name of the bb, to tool + genome + possible adding if multiple +  .bb
        trackName = "".join( ( self.name_gtf, ".bb") )
        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
        with open(myBigBedFilePath, 'w') as bigBedFile:
            subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)

        # Create the Track Object
        self.createTrack(file_path=trackName,
                         track_name=trackName,
                         long_label=self.name_gtf, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
                         track_file=myBigBedFilePath)
        #
        # dataURL = "tracks/%s" % trackName
        #
        # trackDb = TrackDb(
        #     trackName=trackName,
        #     longLabel=self.name_gtf,
        #     shortLabel=self.getShortName( self.name_gtf ),
        #     trackDataURL=dataURL,
        #     trackType='bigBed 12 +',
        #     visibility='dense',
        #     priority=self.priority,
        # )
        # self.track = Track(
        #     trackFile=myBigBedFilePath,
        #     trackDb=trackDb,
        # )

        print("- Gtf %s created" % self.name_gtf)
        #print("- %s created in %s" % (trackName, myBigBedFilePath))