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annotate Bam.py @ 10:acc233161f50 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
author rmarenco
date Thu, 21 Jul 2016 05:58:51 -0400
parents fb5e60d4d18a
children d05236b15f81
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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 super(Bam, self).__init__()
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21 self.track = None
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23 self.input_bam_false_path = input_bam_false_path
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25 self.data_bam = data_bam
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26 # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension
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27 self.name_bam = self.data_bam["name"] + ".bam"
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28 self.priority = self.data_bam["order_index"]
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29 self.index_bam = self.data_bam["index"]
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31 print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam)
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33 # First: Add the bam file
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34 # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
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36 bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
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37 shutil.copyfile(self.input_bam_false_path, bam_file_path)
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39 # Create and add the bam index file to the same folder
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40 name_index_bam = self.name_bam + ".bai"
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41 bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
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42 shutil.copyfile(self.index_bam, bam_index_file_path)
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44 # Create the Track Object
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45 dataURL = "tracks/%s" % self.name_bam
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47 trackDb = TrackDb(
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48 trackName=self.name_bam,
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49 longLabel=self.name_bam,
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50 shortLabel=self.getShortName( self.name_bam ),
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51 trackDataURL=dataURL,
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52 trackType='bam',
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53 visibility='pack',
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54 priority=self.priority,
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55 )
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57 # Return the Bam Track Object
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58 self.track = Track(
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59 trackFile=bam_index_file_path,
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60 trackDb=trackDb,
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61 )
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63 print("- %s created in %s" % (self.name_bam, bam_file_path))
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64 print("- %s created in %s" % (self.index_bam, bam_index_file_path))