Mercurial > repos > juanperin > bwa_wrapper
diff bwa_long/bwa_wrapper.py @ 0:fb4844b6a98e default tip
Migrated tool version 1.0.3 from old tool shed archive to new tool shed repository
| author | juanperin |
|---|---|
| date | Tue, 07 Jun 2011 17:28:32 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa_long/bwa_wrapper.py Tue Jun 07 17:28:32 2011 -0400 @@ -0,0 +1,273 @@ +#!/usr/bin/env python + +""" +Runs BWA on single-end or paired-end data. +Produces a SAM file containing the mappings. +Works with BWA version 0.5.3-0.5.5. + +usage: bwa_wrapper.py [options] + -t, --threads=t: The number of threads to use + -r, --ref=r: The reference genome to use or index + -f, --fastq=f: The (forward) fastq file to use for the mapping + -F, --rfastq=F: The reverse fastq file to use for mapping if paired-end data + -u, --output=u: The file to save the output (SAM format) + -g, --genAlignType=g: The type of pairing (single or paired) + -p, --params=p: Parameter setting to use (pre_set or full) + -s, --fileSource=s: Whether to use a previously indexed reference sequence or one from history (indexed or history) + -n, --maxEditDist=n: Maximum edit distance if integer + -m, --fracMissingAligns=m: Fraction of missing alignments given 2% uniform base error rate if fraction + -o, --maxGapOpens=o: Maximum number of gap opens + -e, --maxGapExtens=e: Maximum number of gap extensions + -d, --disallowLongDel=d: Disallow a long deletion within specified bps + -i, --disallowIndel=i: Disallow indel within specified bps + -l, --seed=l: Take the first specified subsequences + -k, --maxEditDistSeed=k: Maximum edit distance to the seed + -M, --mismatchPenalty=M: Mismatch penalty + -O, --gapOpenPenalty=O: Gap open penalty + -E, --gapExtensPenalty=E: Gap extension penalty + -R, --suboptAlign=R: Proceed with suboptimal alignments even if the top hit is a repeat + -N, --noIterSearch=N: Disable iterative search + -T, --outputTopN=T: Output top specified hits + -S, --maxInsertSize=S: Maximum insert size for a read pair to be considered mapped good + -P, --maxOccurPairing=P: Maximum occurrences of a read for pairings + -D, --dbkey=D: Dbkey for reference genome + -H, --suppressHeader=h: Suppress header +""" + +import optparse, os, shutil, subprocess, sys, tempfile + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +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( '-r', '--ref', dest='ref', help='The reference genome to use or index' ) + parser.add_option( '-f', '--fastq', dest='fastq', help='The (forward) fastq file to use for the mapping' ) + parser.add_option( '-F', '--rfastq', 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='Output top specified hits' ) + 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( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' ) + parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) + (options, args) = parser.parse_args() + # make temp directory for placement of indices + tmp_index_dir = tempfile.mkdtemp() + tmp_dir = tempfile.mkdtemp() + # index if necessary + if options.fileSource == 'history': + 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 = '-a %s' % 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 + # set up aligning and generate aligning command options + if options.params == 'pre_set': + aligning_cmds = '-t %s' % options.threads + 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' % \ + ( editDist, options.maxGapOpens, options.maxGapExtens, options.disallowLongDel, + options.disallowIndel, seed, options.maxEditDistSeed, options.threads, + options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty, + suboptAlign, noIterSearch ) + if options.genAlignType == 'single': + gen_alignment_cmds = '-n %s' % options.outputTopN + elif options.genAlignType == 'paired': + gen_alignment_cmds = '-a %s -o %s' % ( options.maxInsertSize, options.maxOccurPairing ) + else: + 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, options.fastq, tmp_align_out_name ) + cmd2b = '' + if options.genAlignType == 'paired': + cmd2b = 'bwa aln %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.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, options.fastq, options.rfastq, options.output ) + elif options.genAlignType == 'single': + cmd3 = 'bwa samse %s %s %s %s >> %s' % ( gen_alignment_cmds, ref_file_name, tmp_align_out_name, options.fastq, options.output ) + else: + cmd2 = 'sleep 1' + cmd2b = 'sleep 1' + cmd3 = 'bwa bwasw %s %s %s >> %s' % ( gen_alignment_cmds, ref_file_name, options.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__()