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annotate Bed.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 Bed( Datatype ):
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14 def __init__( self, inputBedGeneric, data_bed_generic,
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15 inputFastaFile, extra_files_path, tool_directory ):
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16 super(Bed, self).__init__(
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17 inputFastaFile, extra_files_path, tool_directory
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18 )
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20 self.track = None
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22 self.inputBedGeneric = inputBedGeneric
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24 self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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25 self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
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26 self.twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
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28 self.data_bed_generic = data_bed_generic
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29 self.name_bed_generic = self.data_bed_generic["name"]
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30 self.priority = self.data_bed_generic["order_index"]
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32 # Sort processing
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33 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
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35 # Generate the chrom.sizes
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36 # TODO: Isolate in a function
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37 # We first get the twoBit Infos
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38 subtools.twoBitInfo(self.twoBitFile.name, self.twoBitInfoFile.name)
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40 # Then we get the output to inject into the sort
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41 # TODO: Check if no errors
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42 subtools.sortChromSizes(self.twoBitInfoFile.name, self.chromSizesFile.name)
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44 # bedToBigBed processing
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45 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
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46 trackName = "".join( ( self.name_bed_generic, ".bb") )
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48 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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49 with open(myBigBedFilePath, 'w') as self.bigBedFile:
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50 subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name)
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52 # Create the Track Object
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53 dataURL = "tracks/%s" % trackName
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55 trackDb = TrackDb(
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56 trackName=trackName,
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57 longLabel=self.name_bed_generic,
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58 shortLabel=self.getShortName(self.name_bed_generic),
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59 trackDataURL=dataURL,
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60 trackType='bigBed',
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61 visibility='dense',
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62 thickDrawItem='on',
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63 priority=self.priority,
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64 )
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66 # Return the BigBed track
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67 self.track = Track(
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68 trackFile=myBigBedFilePath,
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69 trackDb=trackDb,
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70 )
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72 print("- %s created in %s" % (trackName, myBigBedFilePath))