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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3
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4 """
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5 A wrapper script for slicing a BAM file by provided BED file using SAMTools.
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6 %prog input_filename.sam output_filename.bam
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7 """
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8 #TODO: Confirm that the sort is necessary e.g. if input regions are out of order
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9
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10
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11 import sys, optparse, os, tempfile, subprocess, shutil
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12
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13 CHUNK_SIZE = 2**20 #1mb
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14
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15 def cleanup_before_exit( tmp_dir ):
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16 if tmp_dir and os.path.exists( tmp_dir ):
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17 shutil.rmtree( tmp_dir )
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18
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19 def __main__():
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20 #Parse Command Line
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21 parser = optparse.OptionParser()
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22 (options, args) = parser.parse_args()
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23
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24 assert len( args ) == 4, "Invalid command line: samtools_slice_bam.py input.bam input.bam.bai input.interval output.bam"
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25 input_bam_filename, input_index_filename, input_interval_filename, output_bam_filename = args
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26
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27 tmp_dir = tempfile.mkdtemp( prefix='tmp-samtools_slice_bam-' )
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28
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29 tmp_input_bam_filename = os.path.join( tmp_dir, 'input_bam.bam' )
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30 os.symlink( input_bam_filename, tmp_input_bam_filename )
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31 os.symlink( input_index_filename, "%s.bai" % tmp_input_bam_filename )
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32
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33 #Slice BAM
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34 unsorted_bam_filename = os.path.join( tmp_dir, 'unsorted.bam' )
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35 unsorted_stderr_filename = os.path.join( tmp_dir, 'unsorted.stderr' )
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36 cmd = 'samtools view -b -L "%s" "%s" > "%s"' % ( input_interval_filename, tmp_input_bam_filename, unsorted_bam_filename )
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37 proc = subprocess.Popen( args=cmd, stderr=open( unsorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
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38 return_code = proc.wait()
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39 if return_code:
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40 stderr_target = sys.stderr
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41 else:
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42 stderr_target = sys.stdout
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43 stderr = open( unsorted_stderr_filename )
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44 while True:
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45 chunk = stderr.read( CHUNK_SIZE )
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46 if chunk:
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47 stderr_target.write( chunk )
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48 else:
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49 break
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50 stderr.close()
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51
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52 #sort sam, so indexing will not fail
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53 #TODO: confirm if sorting is necessary (is original BAM order maintained, or does the output follow the order of input intervals?)
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54 sorted_stderr_filename = os.path.join( tmp_dir, 'sorted.stderr' )
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55 sorting_prefix = os.path.join( tmp_dir, 'sorted_bam' )
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56 cmd = 'samtools sort -o "%s" "%s" > "%s"' % ( unsorted_bam_filename, sorting_prefix, output_bam_filename )
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57 proc = subprocess.Popen( args=cmd, stderr=open( sorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
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58 return_code = proc.wait()
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59
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60 if return_code:
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61 stderr_target = sys.stderr
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62 else:
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63 stderr_target = sys.stdout
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64 stderr = open( sorted_stderr_filename )
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65 while True:
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66 chunk = stderr.read( CHUNK_SIZE )
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67 if chunk:
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68 stderr_target.write( chunk )
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69 else:
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70 break
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71 stderr.close()
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72
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73 cleanup_before_exit( tmp_dir )
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74
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75 if __name__=="__main__": __main__()
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