Mercurial > repos > rmarenco > hubarchivecreator
diff Bed.py @ 1:fb5e60d4d18a draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author | rmarenco |
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date | Wed, 13 Jul 2016 13:36:37 -0400 |
parents | |
children | acc233161f50 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Bed.py Wed Jul 13 13:36:37 2016 -0400 @@ -0,0 +1,72 @@ +#!/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 Bed( Datatype ): + def __init__( self, inputBedGeneric, data_bed_generic, + inputFastaFile, extra_files_path, tool_directory ): + super(Bed, self).__init__( + inputFastaFile, extra_files_path, tool_directory + ) + + self.track = None + + self.inputBedGeneric = inputBedGeneric + + self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") + self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes") + self.twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0) + + self.data_bed_generic = data_bed_generic + self.name_bed_generic = self.data_bed_generic["name"] + self.priority = self.data_bed_generic["order_index"] + + # Sort processing + subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) + + # Generate the chrom.sizes + # TODO: Isolate in a function + # We first get the twoBit Infos + subtools.twoBitInfo(self.twoBitFile.name, self.twoBitInfoFile.name) + + # Then we get the output to inject into the sort + # TODO: Check if no errors + subtools.sortChromSizes(self.twoBitInfoFile.name, self.chromSizesFile.name) + + # bedToBigBed processing + # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb + trackName = "".join( ( self.name_bed_generic, ".bb") ) + + myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) + with open(myBigBedFilePath, 'w') as self.bigBedFile: + subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name) + + # Create the Track Object + dataURL = "tracks/%s" % trackName + + trackDb = TrackDb( + trackName=trackName, + longLabel=self.name_bed_generic, + shortLabel=self.getShortName(self.name_bed_generic), + trackDataURL=dataURL, + trackType='bigBed', + visibility='dense', + thickDrawItem='on', + priority=self.priority, + ) + + # Return the BigBed track + self.track = Track( + trackFile=myBigBedFilePath, + trackDb=trackDb, + ) + + print("- %s created in %s" % (trackName, myBigBedFilePath))