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338 lines
17 KiB
Python
338 lines
17 KiB
Python
#!/usr/bin/env python
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"""
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Runs BWA on single-end or paired-end data.
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Produces a SAM file containing the mappings.
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Works with BWA version 0.5.9.
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usage: bwa_wrapper.py [options]
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See below for options
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"""
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import optparse, os, shutil, 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 check_is_double_encoded( fastq ):
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# check that first read is bases, not one base followed by numbers
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bases = [ 'A', 'C', 'G', 'T', 'a', 'c', 'g', 't', 'N' ]
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nums = [ '0', '1', '2', '3' ]
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for line in file( fastq, 'rb'):
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if not line.strip() or line.startswith( '@' ):
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continue
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if len( [ b for b in line.strip() if b in nums ] ) > 0:
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return False
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elif line.strip()[0] in bases and len( [ b for b in line.strip() if b in bases ] ) == len( line.strip() ):
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return True
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else:
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raise Exception, 'First line in first read does not appear to be a valid FASTQ read in either base-space or color-space'
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raise Exception, 'There is no non-comment and non-blank line in your FASTQ file'
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def __main__():
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#Parse Command Line
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parser = optparse.OptionParser()
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parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to use' )
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parser.add_option( '-c', '--color-space', dest='color_space', action='store_true', help='If the input files are SOLiD format' )
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parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
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parser.add_option( '-f', '--input1', dest='fastq', help='The (forward) fastq file to use for the mapping' )
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parser.add_option( '-F', '--input2', dest='rfastq', help='The reverse fastq file to use for mapping if paired-end data' )
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parser.add_option( '-u', '--output', dest='output', help='The file to save the output (SAM format)' )
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parser.add_option( '-g', '--genAlignType', dest='genAlignType', help='The type of pairing (single or paired)' )
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parser.add_option( '-p', '--params', dest='params', help='Parameter setting to use (pre_set or full)' )
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parser.add_option( '-s', '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one form history (indexed or history)' )
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parser.add_option( '-n', '--maxEditDist', dest='maxEditDist', help='Maximum edit distance if integer' )
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parser.add_option( '-m', '--fracMissingAligns', dest='fracMissingAligns', help='Fraction of missing alignments given 2% uniform base error rate if fraction' )
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parser.add_option( '-o', '--maxGapOpens', dest='maxGapOpens', help='Maximum number of gap opens' )
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parser.add_option( '-e', '--maxGapExtens', dest='maxGapExtens', help='Maximum number of gap extensions' )
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parser.add_option( '-d', '--disallowLongDel', dest='disallowLongDel', help='Disallow a long deletion within specified bps' )
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parser.add_option( '-i', '--disallowIndel', dest='disallowIndel', help='Disallow indel within specified bps' )
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parser.add_option( '-l', '--seed', dest='seed', help='Take the first specified subsequences' )
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parser.add_option( '-k', '--maxEditDistSeed', dest='maxEditDistSeed', help='Maximum edit distance to the seed' )
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parser.add_option( '-M', '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' )
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parser.add_option( '-O', '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' )
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parser.add_option( '-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' )
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parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', help='Proceed with suboptimal alignments even if the top hit is a repeat' )
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parser.add_option( '-N', '--noIterSearch', dest='noIterSearch', help='Disable iterative search' )
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parser.add_option( '-T', '--outputTopN', dest='outputTopN', help='Maximum number of alignments to output in the XA tag for reads paired properly' )
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parser.add_option( '', '--outputTopNDisc', dest='outputTopNDisc', help='Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)' )
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parser.add_option( '-S', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good' )
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parser.add_option( '-P', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings' )
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parser.add_option( '', '--rgid', dest='rgid', help='Read group identifier' )
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parser.add_option( '', '--rgcn', dest='rgcn', help='Sequencing center that produced the read' )
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parser.add_option( '', '--rgds', dest='rgds', help='Description' )
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parser.add_option( '', '--rgdt', dest='rgdt', help='Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)' )
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parser.add_option( '', '--rgfo', dest='rgfo', help='Flow order' )
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parser.add_option( '', '--rgks', dest='rgks', help='The array of nucleotide bases that correspond to the key sequence of each read' )
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parser.add_option( '', '--rglb', dest='rglb', help='Library name' )
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parser.add_option( '', '--rgpg', dest='rgpg', help='Programs used for processing the read group' )
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parser.add_option( '', '--rgpi', dest='rgpi', help='Predicted median insert size' )
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parser.add_option( '', '--rgpl', dest='rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT' and 'PACBIO' ], help='Platform/technology used to produce the reads' )
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parser.add_option( '', '--rgpu', dest='rgpu', help='Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)' )
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parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' )
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parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' )
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parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )
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parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
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(options, args) = parser.parse_args()
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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='bwa 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( 'BWA %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 BWA version\n' )
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# check for color space fastq that's not double-encoded and exit if appropriate
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if options.color_space:
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if not check_is_double_encoded( options.fastq ):
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stop_err( 'Your file must be double-encoded (it must be converted from "numbers" to "bases"). See the help section for details' )
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if options.genAlignType == 'paired':
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if not check_is_double_encoded( options.rfastq ):
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stop_err( 'Your reverse reads file must also be double-encoded (it must be converted from "numbers" to "bases"). See the help section for details' )
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fastq = options.fastq
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if options.rfastq:
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rfastq = options.rfastq
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# set color space variable
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if options.color_space:
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color_space = '-c'
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else:
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color_space = ''
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# make temp directory for placement of indices
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tmp_index_dir = tempfile.mkdtemp()
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tmp_dir = tempfile.mkdtemp()
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# index if necessary
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if options.fileSource == 'history' and not options.do_not_build_index:
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ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
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ref_file_name = ref_file.name
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ref_file.close()
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os.symlink( options.ref, ref_file_name )
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# determine which indexing algorithm to use, based on size
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try:
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size = os.stat( options.ref ).st_size
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if size <= 2**30:
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indexingAlg = 'is'
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else:
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indexingAlg = 'bwtsw'
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except:
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indexingAlg = 'is'
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indexing_cmds = '%s -a %s' % ( color_space, indexingAlg )
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cmd1 = 'bwa index %s %s' % ( indexing_cmds, ref_file_name )
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try:
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tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, 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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except Exception, e:
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# clean up temp dirs
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if os.path.exists( tmp_index_dir ):
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shutil.rmtree( tmp_index_dir )
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if os.path.exists( tmp_dir ):
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shutil.rmtree( tmp_dir )
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stop_err( 'Error indexing reference sequence. ' + str( e ) )
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else:
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ref_file_name = options.ref
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# set up aligning and generate aligning command options
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if options.params == 'pre_set':
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aligning_cmds = '-t %s %s' % ( options.threads, color_space )
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gen_alignment_cmds = ''
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else:
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if options.maxEditDist != '0':
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editDist = options.maxEditDist
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else:
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editDist = options.fracMissingAligns
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if options.seed != '-1':
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seed = '-l %s' % options.seed
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else:
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seed = ''
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if options.suboptAlign == 'true':
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suboptAlign = '-R'
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else:
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suboptAlign = ''
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if options.noIterSearch == 'true':
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noIterSearch = '-N'
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else:
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noIterSearch = ''
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aligning_cmds = '-n %s -o %s -e %s -d %s -i %s %s -k %s -t %s -M %s -O %s -E %s %s %s %s' % \
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( editDist, options.maxGapOpens, options.maxGapExtens, options.disallowLongDel,
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options.disallowIndel, seed, options.maxEditDistSeed, options.threads,
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options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty,
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suboptAlign, noIterSearch, color_space )
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if options.genAlignType == 'paired':
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gen_alignment_cmds = '-a %s -o %s' % ( options.maxInsertSize, options.maxOccurPairing )
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if options.outputTopNDisc:
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gen_alignment_cmds += ' -N %s' % options.outputTopNDisc
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else:
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gen_alignment_cmds = ''
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if options.rgid:
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if not options.rglb or not options.rgpl or not options.rgsm:
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stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )
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readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm )
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if options.rgcn:
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readGroup += '\tCN:%s' % options.rgcn
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if options.rgds:
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readGroup += '\tDS:%s' % options.rgds
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if options.rgdt:
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readGroup += '\tDT:%s' % options.rgdt
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if options.rgfo:
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readGroup += '\tFO:%s' % options.rgfo
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if options.rgks:
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readGroup += '\tKS:%s' % options.rgks
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if options.rgpg:
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readGroup += '\tPG:%s' % options.rgpg
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if options.rgpi:
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readGroup += '\tPI:%s' % options.rgpi
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if options.rgpu:
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readGroup += '\tPU:%s' % options.rgpu
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gen_alignment_cmds += ' -r "%s"' % readGroup
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if options.outputTopN:
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gen_alignment_cmds += ' -n %s' % options.outputTopN
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# set up output files
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tmp_align_out = tempfile.NamedTemporaryFile( dir=tmp_dir )
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tmp_align_out_name = tmp_align_out.name
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tmp_align_out.close()
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tmp_align_out2 = tempfile.NamedTemporaryFile( dir=tmp_dir )
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tmp_align_out2_name = tmp_align_out2.name
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tmp_align_out2.close()
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# prepare actual aligning and generate aligning commands
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cmd2 = 'bwa aln %s %s %s > %s' % ( aligning_cmds, ref_file_name, fastq, tmp_align_out_name )
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cmd2b = ''
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if options.genAlignType == 'paired':
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cmd2b = 'bwa aln %s %s %s > %s' % ( aligning_cmds, ref_file_name, rfastq, tmp_align_out2_name )
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cmd3 = 'bwa sampe %s %s %s %s %s %s >> %s' % ( gen_alignment_cmds, ref_file_name, tmp_align_out_name, tmp_align_out2_name, fastq, rfastq, options.output )
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else:
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cmd3 = 'bwa samse %s %s %s %s >> %s' % ( gen_alignment_cmds, ref_file_name, tmp_align_out_name, fastq, options.output )
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# perform alignments
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buffsize = 1048576
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try:
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# need to nest try-except in try-finally to handle 2.4
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try:
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# align
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try:
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tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, 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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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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except Exception, e:
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raise Exception, 'Error aligning sequence. ' + str( e )
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# and again if paired data
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try:
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if cmd2b:
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tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=cmd2b, shell=True, cwd=tmp_dir, 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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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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except Exception, e:
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raise Exception, 'Error aligning second sequence. ' + str( e )
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# generate align
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try:
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tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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tmp_stderr = open( tmp, 'wb' )
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proc = subprocess.Popen( args=cmd3, shell=True, cwd=tmp_dir, 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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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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except Exception, e:
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raise Exception, 'Error generating alignments. ' + str( e )
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# remove header if necessary
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if options.suppressHeader == 'true':
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tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
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tmp_out_name = tmp_out.name
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tmp_out.close()
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try:
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shutil.move( options.output, tmp_out_name )
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except Exception, e:
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raise Exception, 'Error moving output file before removing headers. ' + str( e )
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fout = file( options.output, 'w' )
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for line in file( tmp_out.name, 'r' ):
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if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):
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fout.write( line )
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fout.close()
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# check that there are results in the output file
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if os.path.getsize( options.output ) > 0:
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sys.stdout.write( 'BWA run on %s-end data' % options.genAlignType )
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else:
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raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.'
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except Exception, e:
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stop_err( 'The alignment failed.\n' + str( e ) )
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finally:
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# clean up temp dir
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if os.path.exists( tmp_index_dir ):
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shutil.rmtree( tmp_index_dir )
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if os.path.exists( tmp_dir ):
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shutil.rmtree( tmp_dir )
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if __name__=="__main__": __main__()
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