[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | """ |
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| 4 | Merges any number of BAM files |
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| 5 | usage: %prog [options] |
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| 6 | input1 |
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| 7 | output1 |
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| 8 | input2 |
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| 9 | [input3[,input4[,input5[,...]]]] |
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| 10 | """ |
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| 11 | |
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| 12 | import os, subprocess, sys, tempfile |
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| 13 | |
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| 14 | def stop_err( msg ): |
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| 15 | sys.stderr.write( '%s\n' % msg ) |
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| 16 | sys.exit() |
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| 17 | |
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| 18 | def __main__(): |
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| 19 | infile = sys.argv[1] |
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| 20 | outfile = sys.argv[2] |
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| 21 | if len( sys.argv ) < 3: |
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| 22 | stop_err( 'There are not enough files to merge' ) |
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| 23 | filenames = sys.argv[3:] |
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| 24 | cmd = 'samtools merge %s %s %s' % ( outfile, infile, ' '.join( filenames ) ) |
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| 25 | tmp = tempfile.NamedTemporaryFile().name |
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| 26 | try: |
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| 27 | tmp_stderr = open( tmp, 'wb' ) |
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| 28 | proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) |
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| 29 | returncode = proc.wait() |
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| 30 | tmp_stderr.close() |
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| 31 | # get stderr, allowing for case where it's very large |
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| 32 | tmp_stderr = open( tmp, 'rb' ) |
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| 33 | stderr = '' |
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| 34 | buffsize = 1048576 |
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| 35 | try: |
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| 36 | while True: |
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| 37 | stderr += tmp_stderr.read( buffsize ) |
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| 38 | if not stderr or len( stderr ) % buffsize != 0: |
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| 39 | break |
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| 40 | except OverflowError: |
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| 41 | pass |
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| 42 | tmp_stderr.close() |
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| 43 | if returncode != 0: |
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| 44 | raise Exception, stderr |
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| 45 | if os.path.exists( tmp ): |
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| 46 | os.unlink( tmp ) |
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| 47 | except Exception, e: |
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| 48 | if os.path.exists( tmp ): |
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| 49 | os.unlink( tmp ) |
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| 50 | stop_err( 'Error running SAMtools merge tool\n' + str( e ) ) |
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| 51 | if os.path.getsize( outfile ) > 0: |
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| 52 | sys.stdout.write( '%s files merged.' % ( len( sys.argv ) - 2 ) ) |
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| 53 | else: |
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| 54 | stop_err( 'The output file is empty, there may be an error with one of your input files.' ) |
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| 55 | |
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| 56 | if __name__ == "__main__" : __main__() |
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