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annotate Bam.py @ 4:1b653b332695 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Thu, 14 Jul 2016 14:55:12 -0400
parents fb5e60d4d18a
children acc233161f50
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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4 """
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5 Class to handle Bam files to UCSC TrackHub
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6 """
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8 import os
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9 import shutil
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11 from Datatype import Datatype
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12 from Track import Track
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13 from TrackDb import TrackDb
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14 from util import subtools
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17 class Bam( Datatype ):
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18 def __init__( self, input_bam_false_path, data_bam ,
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19 inputFastaFile, extra_files_path, tool_directory ):
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20 super(Bam, self).__init__( input_fasta_file=inputFastaFile,
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21 extra_files_path=extra_files_path,
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22 tool_directory=tool_directory,
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23 )
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25 self.track = None
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27 self.input_bam_false_path = input_bam_false_path
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29 self.data_bam = data_bam
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30 # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension
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31 self.name_bam = self.data_bam["name"] + ".bam"
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32 self.priority = self.data_bam["order_index"]
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33 self.index_bam = self.data_bam["index"]
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35 print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam)
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37 # First: Add the bam file
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38 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
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40 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
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41 shutil.copyfile(self.input_bam_false_path, bam_file_path)
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43 # Create and add the bam index file to the same folder
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44 name_index_bam = self.name_bam + ".bai"
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45 bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
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46 shutil.copyfile(self.index_bam, bam_index_file_path)
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48 # Create the Track Object
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49 dataURL = "tracks/%s" % self.name_bam
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51 trackDb = TrackDb(
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52 trackName=self.name_bam,
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53 longLabel=self.name_bam,
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54 shortLabel=self.getShortName( self.name_bam ),
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55 trackDataURL=dataURL,
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56 trackType='bam',
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57 visibility='pack',
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58 priority=self.priority,
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59 )
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61 # Return the Bam Track Object
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62 self.track = Track(
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63 trackFile=bam_index_file_path,
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64 trackDb=trackDb,
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65 )
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67 print("- %s created in %s" % (self.name_bam, bam_file_path))
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68 print("- %s created in %s" % (self.index_bam, bam_index_file_path))