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75 lines
2.3 KiB
Python
75 lines
2.3 KiB
Python
#!/usr/bin/env python
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"""
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Merges any number of BAM files
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usage: %prog [options]
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input1
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output1
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input2
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[input3[,input4[,input5[,...]]]]
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"""
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import os, subprocess, sys, tempfile
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def stop_err( msg ):
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sys.stderr.write( '%s\n' % msg )
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sys.exit()
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def __main__():
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infile = sys.argv[1]
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outfile = sys.argv[2]
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if len( sys.argv ) < 3:
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stop_err( 'There are not enough files to merge' )
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filenames = sys.argv[3:]
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# output version # of tool
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try:
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tmp = tempfile.NamedTemporaryFile().name
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tmp_stdout = open( tmp, 'wb' )
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proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
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tmp_stdout.close()
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returncode = proc.wait()
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stdout = None
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for line in open( tmp_stdout.name, 'rb' ):
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if line.lower().find( 'version' ) >= 0:
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stdout = line.strip()
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break
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if stdout:
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sys.stdout.write( 'Samtools %s\n' % stdout )
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else:
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raise Exception
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except:
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sys.stdout.write( 'Could not determine Samtools version\n' )
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cmd = 'samtools merge %s %s %s' % ( outfile, infile, ' '.join( filenames ) )
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tmp = tempfile.NamedTemporaryFile().name
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try:
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
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returncode = proc.wait()
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tmp_stderr.close()
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# get stderr, allowing for case where it's very large
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tmp_stderr = open( tmp, 'rb' )
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stderr = ''
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buffsize = 1048576
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try:
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while True:
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stderr += tmp_stderr.read( buffsize )
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if not stderr or len( stderr ) % buffsize != 0:
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break
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except OverflowError:
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pass
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tmp_stderr.close()
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if returncode != 0:
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raise Exception, stderr
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if os.path.exists( tmp ):
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os.unlink( tmp )
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except Exception, e:
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if os.path.exists( tmp ):
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os.unlink( tmp )
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stop_err( 'Error running SAMtools merge tool\n' + str( e ) )
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if os.path.getsize( outfile ) > 0:
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sys.stdout.write( '%s files merged.' % ( len( sys.argv ) - 2 ) )
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else:
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stop_err( 'The output file is empty, there may be an error with one of your input files.' )
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if __name__ == "__main__" : __main__()
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