view bwa_wrapper.py @ 0:d6ba40f6c824

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#!/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
import glob 
import gzip, zipfile, tarfile

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( '-u', '--output', dest='output', help='The file to save the output (SAM format)' )
    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', default=None, 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()

    tmp_input_dir = tempfile.mkdtemp()
    tmp_output_dir= tempfile.mkdtemp()


    myarchive = zipfile.ZipFile(options.fastq, 'r', allowZip64=True)
    myarchive.extractall(tmp_input_dir)

    for fastq in glob.glob(tmp_input_dir+'/*'):

	    sam_output_file=tmp_output_dir+'/'+os.path.splitext(os.path.basename(fastq))[0]+'.sam'
	    create_sam=open(sam_output_file, "w")
	    create_sam.close()

	    # 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:
		    suboptAlign = '-R "%s"' % ( options.suboptAlign )
		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

		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 = ''
	    cmd3 = 'bwa samse %s %s %s %s >> %s' % ( gen_alignment_cmds, ref_file_name, tmp_align_out_name, fastq, sam_output_file )
	    # 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( sam_output_file, tmp_out_name )
			except Exception, e:
			    raise Exception, 'Error moving output file before removing headers. ' + str( e )
			fout = file( sam_output_file, '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( sam_output_file ) > 0:
			sys.stdout.write( 'BWA run on single-end data')
		    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 )	

    # put all in an archive
    mytotalzipfile=zipfile.ZipFile(options.output, 'w', allowZip64=True)
    os.chdir(tmp_output_dir)
    for samfile in glob.glob(tmp_output_dir+'/*'):
	mytotalzipfile.write(os.path.basename(samfile))


if __name__=="__main__": __main__()