Mercurial > repos > rmarenco > hubarchivecreator
diff Gtf.py @ 10:acc233161f50 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
author | rmarenco |
---|---|
date | Thu, 21 Jul 2016 05:58:51 -0400 |
parents | fb5e60d4d18a |
children | d05236b15f81 |
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--- a/Gtf.py Wed Jul 20 12:29:08 2016 -0400 +++ b/Gtf.py Thu Jul 21 05:58:51 2016 -0400 @@ -11,11 +11,9 @@ class Gtf( Datatype ): - def __init__( self, input_gtf_false_path, data_gtf, - input_fasta_file, extra_files_path, tool_directory ): - super(Gtf, self).__init__( input_fasta_file=input_fasta_file, - extra_files_path=extra_files_path, - tool_directory=tool_directory ) + def __init__( self, input_gtf_false_path, data_gtf): + + super(Gtf, self).__init__() self.track = None @@ -30,9 +28,6 @@ unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed") sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") - twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0) - chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes") - # GtfToGenePred subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name) @@ -43,20 +38,12 @@ # Sort processing subtools.sort(unsortedBedFile.name, sortedBedFile.name) - # TODO: Chehck if the twoBitInfo / ChromSizes is redundant and make an intermediate class - # Generate the twoBitInfo - subtools.twoBitInfo(self.twoBitFile.name, twoBitInfoFile.name) - - # Then we get the output to generate the chromSizes - # TODO: Check if no errors - subtools.sortChromSizes(twoBitInfoFile.name, chromSizesFile.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, chromSizesFile.name, bigBedFile.name) + subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name) # Create the Track Object dataURL = "tracks/%s" % trackName