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annotate BedSimpleRepeats.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
rmarenco
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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 from Datatype import Datatype
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7 from Track import Track
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8 from TrackDb import TrackDb
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9 from util import subtools
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12 class BedSimpleRepeats( Datatype ):
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13 def __init__( self, input_bed_simple_repeats_false_path, data_bed_simple_repeats,
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14 input_fasta_file, extra_files_path, tool_directory ):
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16 super(BedSimpleRepeats, self).__init__(
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17 input_fasta_file, extra_files_path, tool_directory
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18 )
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20 self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path
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21 self.name_bed_simple_repeats = data_bed_simple_repeats["name"]
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22 self.priority = data_bed_simple_repeats["order_index"]
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24 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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25 twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
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26 chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
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28 # Sort processing
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29 subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)
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31 # TODO: Regroup in an mother class which handles the Chrom.sizes creation with Gff3 and Gtf
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32 # Generate the chrom.sizes
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34 subtools.twoBitInfo(self.twoBitFile.name, twoBitInfoFile.name)
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36 # Then we get the output to inject into the sort
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37 # TODO: Check if no errors
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38 subtools.sortChromSizes(twoBitInfoFile.name, chromSizesFile.name)
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40 # bedToBigBed processing
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41 # TODO: Change the name of the bb, to tool + genome + .bb
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42 trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
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43 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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44 auto_sql_option = "%s%s" % ('-as=', os.path.join(self.tool_directory, 'trf_simpleRepeat.as'))
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45 with open(myBigBedFilePath, 'w') as bigBedFile:
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46 subtools.bedToBigBed(sortedBedFile.name, chromSizesFile.name, bigBedFile.name,
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47 typeOption='-type=bed4+12',
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48 autoSql=auto_sql_option)
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49
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50 # Create the Track Object
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51 dataURL = "tracks/%s" % trackName
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52
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53 trackDb = TrackDb(
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54 trackName=trackName,
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55 longLabel=self.name_bed_simple_repeats,
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56 shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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57 trackDataURL=dataURL,
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58 trackType='bigBed 4 +',
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59 visibility='dense',
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60 priority=self.priority,
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61 )
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63 self.track = Track(
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64 trackFile=myBigBedFilePath,
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65 trackDb=trackDb,
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66 )
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68 print("- %s created in %s" % (trackName, myBigBedFilePath))