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annotate Gtf.py @ 1:fb5e60d4d18a draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Wed, 13 Jul 2016 13:36:37 -0400
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children acc233161f50
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fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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1 #!/usr/bin/python
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3 import os
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4 import tempfile
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6 # Internal dependencies
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7 from Datatype import Datatype
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8 from Track import Track
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9 from TrackDb import TrackDb
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10 from util import subtools
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13 class Gtf( Datatype ):
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14 def __init__( self, input_gtf_false_path, data_gtf,
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15 input_fasta_file, extra_files_path, tool_directory ):
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16 super(Gtf, self).__init__( input_fasta_file=input_fasta_file,
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17 extra_files_path=extra_files_path,
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18 tool_directory=tool_directory )
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20 self.track = None
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22 self.input_gtf_false_path = input_gtf_false_path
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23 self.name_gtf = data_gtf["name"]
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24 self.priority = data_gtf["order_index"]
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26 print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
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28 # TODO: See if we need these temporary files as part of the generated files
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29 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
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30 unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
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31 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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33 twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
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34 chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
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36 # GtfToGenePred
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37 subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name)
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39 # TODO: From there, refactor because common use with Gff3.py
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40 # genePredToBed processing
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41 subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)
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43 # Sort processing
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44 subtools.sort(unsortedBedFile.name, sortedBedFile.name)
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46 # TODO: Chehck if the twoBitInfo / ChromSizes is redundant and make an intermediate class
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47 # Generate the twoBitInfo
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48 subtools.twoBitInfo(self.twoBitFile.name, twoBitInfoFile.name)
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50 # Then we get the output to generate the chromSizes
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51 # TODO: Check if no errors
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52 subtools.sortChromSizes(twoBitInfoFile.name, chromSizesFile.name)
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54 # bedToBigBed processing
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55 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
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56 trackName = "".join( ( self.name_gtf, ".bb") )
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57 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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58 with open(myBigBedFilePath, 'w') as bigBedFile:
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59 subtools.bedToBigBed(sortedBedFile.name, chromSizesFile.name, bigBedFile.name)
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61 # Create the Track Object
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62 dataURL = "tracks/%s" % trackName
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63
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64 trackDb = TrackDb(
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65 trackName=trackName,
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66 longLabel=self.name_gtf,
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67 shortLabel=self.getShortName( self.name_gtf ),
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68 trackDataURL=dataURL,
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69 trackType='bigBed 12 +',
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70 visibility='dense',
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71 priority=self.priority,
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72 )
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73 self.track = Track(
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74 trackFile=myBigBedFilePath,
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75 trackDb=trackDb,
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76 )
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78 print("- %s created in %s" % (trackName, myBigBedFilePath))