/tools/sr_mapping/bwa_wrapper.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 342 lines · 296 code · 12 blank · 34 comment · 113 complexity · 3a9aba466fb4a8a8029ac3c4fcccf412 MD5 · raw file
- #!/usr/bin/env python
- """
- Runs BWA on single-end or paired-end data.
- Produces a SAM file containing the mappings.
- Works with BWA version 0.5.9.
- usage: bwa_wrapper.py [options]
- See below for options
- """
- import optparse, os, shutil, subprocess, sys, tempfile
- def stop_err( msg ):
- sys.stderr.write( '%s\n' % msg )
- sys.exit()
- def check_is_double_encoded( fastq ):
- # check that first read is bases, not one base followed by numbers
- bases = [ 'A', 'C', 'G', 'T', 'a', 'c', 'g', 't', 'N' ]
- nums = [ '0', '1', '2', '3' ]
- for line in file( fastq, 'rb'):
- if not line.strip() or line.startswith( '@' ):
- continue
- if len( [ b for b in line.strip() if b in nums ] ) > 0:
- return False
- elif line.strip()[0] in bases and len( [ b for b in line.strip() if b in bases ] ) == len( line.strip() ):
- return True
- else:
- raise Exception, 'First line in first read does not appear to be a valid FASTQ read in either base-space or color-space'
- raise Exception, 'There is no non-comment and non-blank line in your FASTQ file'
- def __main__():
- #Parse Command Line
- parser = optparse.OptionParser()
- parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to use' )
- parser.add_option( '-c', '--color-space', dest='color_space', action='store_true', help='If the input files are SOLiD format' )
- parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' )
- parser.add_option( '-f', '--input1', dest='fastq', help='The (forward) fastq file to use for the mapping' )
- parser.add_option( '-F', '--input2', dest='rfastq', help='The reverse fastq file to use for mapping if paired-end data' )
- parser.add_option( '-u', '--output', dest='output', help='The file to save the output (SAM format)' )
- parser.add_option( '-g', '--genAlignType', dest='genAlignType', help='The type of pairing (single or paired)' )
- parser.add_option( '-p', '--params', dest='params', help='Parameter setting to use (pre_set or full)' )
- parser.add_option( '-s', '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one form history (indexed or history)' )
- parser.add_option( '-n', '--maxEditDist', dest='maxEditDist', help='Maximum edit distance if integer' )
- parser.add_option( '-m', '--fracMissingAligns', dest='fracMissingAligns', help='Fraction of missing alignments given 2% uniform base error rate if fraction' )
- parser.add_option( '-o', '--maxGapOpens', dest='maxGapOpens', help='Maximum number of gap opens' )
- parser.add_option( '-e', '--maxGapExtens', dest='maxGapExtens', help='Maximum number of gap extensions' )
- parser.add_option( '-d', '--disallowLongDel', dest='disallowLongDel', help='Disallow a long deletion within specified bps' )
- parser.add_option( '-i', '--disallowIndel', dest='disallowIndel', help='Disallow indel within specified bps' )
- parser.add_option( '-l', '--seed', dest='seed', help='Take the first specified subsequences' )
- parser.add_option( '-k', '--maxEditDistSeed', dest='maxEditDistSeed', help='Maximum edit distance to the seed' )
- parser.add_option( '-M', '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' )
- parser.add_option( '-O', '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' )
- parser.add_option( '-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' )
- parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', help='Proceed with suboptimal alignments even if the top hit is a repeat' )
- parser.add_option( '-N', '--noIterSearch', dest='noIterSearch', help='Disable iterative search' )
- parser.add_option( '-T', '--outputTopN', dest='outputTopN', help='Maximum number of alignments to output in the XA tag for reads paired properly' )
- parser.add_option( '', '--outputTopNDisc', dest='outputTopNDisc', help='Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)' )
- parser.add_option( '-S', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good' )
- parser.add_option( '-P', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings' )
- parser.add_option( '', '--rgid', dest='rgid', help='Read group identifier' )
- parser.add_option( '', '--rgcn', dest='rgcn', help='Sequencing center that produced the read' )
- parser.add_option( '', '--rgds', dest='rgds', help='Description' )
- parser.add_option( '', '--rgdt', dest='rgdt', help='Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)' )
- parser.add_option( '', '--rgfo', dest='rgfo', help='Flow order' )
- parser.add_option( '', '--rgks', dest='rgks', help='The array of nucleotide bases that correspond to the key sequence of each read' )
- parser.add_option( '', '--rglb', dest='rglb', help='Library name' )
- parser.add_option( '', '--rgpg', dest='rgpg', help='Programs used for processing the read group' )
- parser.add_option( '', '--rgpi', dest='rgpi', help='Predicted median insert size' )
- parser.add_option( '', '--rgpl', dest='rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT' and 'PACBIO' ], help='Platform/technology used to produce the reads' )
- parser.add_option( '', '--rgpu', dest='rgpu', help='Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)' )
- parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' )
- parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' )
- parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )
- parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
- parser.add_option( '-I', '--illumina1.3', dest='illumina13qual', help='Input FASTQ files have Illuina 1.3 quality scores' )
- (options, args) = parser.parse_args()
- # output version # of tool
- try:
- tmp = tempfile.NamedTemporaryFile().name
- tmp_stdout = open( tmp, 'wb' )
- proc = subprocess.Popen( args='bwa 2>&1', shell=True, stdout=tmp_stdout )
- tmp_stdout.close()
- returncode = proc.wait()
- stdout = None
- for line in open( tmp_stdout.name, 'rb' ):
- if line.lower().find( 'version' ) >= 0:
- stdout = line.strip()
- break
- if stdout:
- sys.stdout.write( 'BWA %s\n' % stdout )
- else:
- raise Exception
- except:
- sys.stdout.write( 'Could not determine BWA version\n' )
- # check for color space fastq that's not double-encoded and exit if appropriate
- if options.color_space:
- if not check_is_double_encoded( options.fastq ):
- stop_err( 'Your file must be double-encoded (it must be converted from "numbers" to "bases"). See the help section for details' )
- if options.genAlignType == 'paired':
- if not check_is_double_encoded( options.rfastq ):
- 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' )
- fastq = options.fastq
- if options.rfastq:
- rfastq = options.rfastq
- # set color space variable
- if options.color_space:
- color_space = '-c'
- else:
- color_space = ''
- # make temp directory for placement of indices
- tmp_index_dir = tempfile.mkdtemp()
- tmp_dir = tempfile.mkdtemp()
- # index if necessary
- if options.fileSource == 'history' and not options.do_not_build_index:
- ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
- ref_file_name = ref_file.name
- ref_file.close()
- os.symlink( options.ref, ref_file_name )
- # determine which indexing algorithm to use, based on size
- try:
- size = os.stat( options.ref ).st_size
- if size <= 2**30:
- indexingAlg = 'is'
- else:
- indexingAlg = 'bwtsw'
- except:
- indexingAlg = 'is'
- indexing_cmds = '%s -a %s' % ( color_space, indexingAlg )
- cmd1 = 'bwa index %s %s' % ( indexing_cmds, ref_file_name )
- try:
- tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
- tmp_stderr = open( tmp, 'wb' )
- proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
- returncode = proc.wait()
- tmp_stderr.close()
- # get stderr, allowing for case where it's very large
- tmp_stderr = open( tmp, 'rb' )
- stderr = ''
- buffsize = 1048576
- try:
- while True:
- stderr += tmp_stderr.read( buffsize )
- if not stderr or len( stderr ) % buffsize != 0:
- break
- except OverflowError:
- pass
- tmp_stderr.close()
- if returncode != 0:
- raise Exception, stderr
- except Exception, e:
- # clean up temp dirs
- if os.path.exists( tmp_index_dir ):
- shutil.rmtree( tmp_index_dir )
- if os.path.exists( tmp_dir ):
- shutil.rmtree( tmp_dir )
- stop_err( 'Error indexing reference sequence. ' + str( e ) )
- else:
- ref_file_name = options.ref
- if options.illumina13qual:
- illumina_quals = "-I"
- else:
- illumina_quals = ""
- # set up aligning and generate aligning command options
- if options.params == 'pre_set':
- aligning_cmds = '-t %s %s %s' % ( options.threads, color_space, illumina_quals )
- gen_alignment_cmds = ''
- else:
- if options.maxEditDist != '0':
- editDist = options.maxEditDist
- else:
- editDist = options.fracMissingAligns
- if options.seed != '-1':
- seed = '-l %s' % options.seed
- else:
- seed = ''
- if options.suboptAlign == 'true':
- suboptAlign = '-R'
- else:
- suboptAlign = ''
- if options.noIterSearch == 'true':
- noIterSearch = '-N'
- else:
- noIterSearch = ''
- 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 %s' % \
- ( editDist, options.maxGapOpens, options.maxGapExtens, options.disallowLongDel,
- options.disallowIndel, seed, options.maxEditDistSeed, options.threads,
- options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty,
- suboptAlign, noIterSearch, color_space, illumina_quals )
- if options.genAlignType == 'paired':
- gen_alignment_cmds = '-a %s -o %s' % ( options.maxInsertSize, options.maxOccurPairing )
- if options.outputTopNDisc:
- gen_alignment_cmds += ' -N %s' % options.outputTopNDisc
- else:
- gen_alignment_cmds = ''
- if options.rgid:
- if not options.rglb or not options.rgpl or not options.rgsm:
- stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )
- readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm )
- if options.rgcn:
- readGroup += '\tCN:%s' % options.rgcn
- if options.rgds:
- readGroup += '\tDS:%s' % options.rgds
- if options.rgdt:
- readGroup += '\tDT:%s' % options.rgdt
- if options.rgfo:
- readGroup += '\tFO:%s' % options.rgfo
- if options.rgks:
- readGroup += '\tKS:%s' % options.rgks
- if options.rgpg:
- readGroup += '\tPG:%s' % options.rgpg
- if options.rgpi:
- readGroup += '\tPI:%s' % options.rgpi
- if options.rgpu:
- readGroup += '\tPU:%s' % options.rgpu
- gen_alignment_cmds += ' -r "%s"' % readGroup
- if options.outputTopN:
- gen_alignment_cmds += ' -n %s' % options.outputTopN
- # set up output files
- tmp_align_out = tempfile.NamedTemporaryFile( dir=tmp_dir )
- tmp_align_out_name = tmp_align_out.name
- tmp_align_out.close()
- tmp_align_out2 = tempfile.NamedTemporaryFile( dir=tmp_dir )
- tmp_align_out2_name = tmp_align_out2.name
- tmp_align_out2.close()
- # prepare actual aligning and generate aligning commands
- cmd2 = 'bwa aln %s %s %s > %s' % ( aligning_cmds, ref_file_name, fastq, tmp_align_out_name )
- cmd2b = ''
- if options.genAlignType == 'paired':
- cmd2b = 'bwa aln %s %s %s > %s' % ( aligning_cmds, ref_file_name, rfastq, tmp_align_out2_name )
- 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 )
- else:
- cmd3 = 'bwa samse %s %s %s %s >> %s' % ( gen_alignment_cmds, ref_file_name, tmp_align_out_name, fastq, options.output )
- # perform alignments
- buffsize = 1048576
- try:
- # need to nest try-except in try-finally to handle 2.4
- try:
- # align
- try:
- tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
- tmp_stderr = open( tmp, 'wb' )
- proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
- returncode = proc.wait()
- tmp_stderr.close()
- # get stderr, allowing for case where it's very large
- tmp_stderr = open( tmp, 'rb' )
- stderr = ''
- try:
- while True:
- stderr += tmp_stderr.read( buffsize )
- if not stderr or len( stderr ) % buffsize != 0:
- break
- except OverflowError:
- pass
- tmp_stderr.close()
- if returncode != 0:
- raise Exception, stderr
- except Exception, e:
- raise Exception, 'Error aligning sequence. ' + str( e )
- # and again if paired data
- try:
- if cmd2b:
- tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
- tmp_stderr = open( tmp, 'wb' )
- proc = subprocess.Popen( args=cmd2b, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
- returncode = proc.wait()
- tmp_stderr.close()
- # get stderr, allowing for case where it's very large
- tmp_stderr = open( tmp, 'rb' )
- stderr = ''
- try:
- while True:
- stderr += tmp_stderr.read( buffsize )
- if not stderr or len( stderr ) % buffsize != 0:
- break
- except OverflowError:
- pass
- tmp_stderr.close()
- if returncode != 0:
- raise Exception, stderr
- except Exception, e:
- raise Exception, 'Error aligning second sequence. ' + str( e )
- # generate align
- try:
- tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
- tmp_stderr = open( tmp, 'wb' )
- proc = subprocess.Popen( args=cmd3, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
- returncode = proc.wait()
- tmp_stderr.close()
- # get stderr, allowing for case where it's very large
- tmp_stderr = open( tmp, 'rb' )
- stderr = ''
- try:
- while True:
- stderr += tmp_stderr.read( buffsize )
- if not stderr or len( stderr ) % buffsize != 0:
- break
- except OverflowError:
- pass
- tmp_stderr.close()
- if returncode != 0:
- raise Exception, stderr
- except Exception, e:
- raise Exception, 'Error generating alignments. ' + str( e )
- # remove header if necessary
- if options.suppressHeader == 'true':
- tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
- tmp_out_name = tmp_out.name
- tmp_out.close()
- try:
- shutil.move( options.output, tmp_out_name )
- except Exception, e:
- raise Exception, 'Error moving output file before removing headers. ' + str( e )
- fout = file( options.output, 'w' )
- for line in file( tmp_out.name, 'r' ):
- if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):
- fout.write( line )
- fout.close()
- # check that there are results in the output file
- if os.path.getsize( options.output ) > 0:
- sys.stdout.write( 'BWA run on %s-end data' % options.genAlignType )
- else:
- 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.'
- except Exception, e:
- stop_err( 'The alignment failed.\n' + str( e ) )
- finally:
- # clean up temp dir
- if os.path.exists( tmp_index_dir ):
- shutil.rmtree( tmp_index_dir )
- if os.path.exists( tmp_dir ):
- shutil.rmtree( tmp_dir )
- if __name__=="__main__": __main__()