diff bwa_wrapper.py @ 0:d6ba40f6c824

first commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa_wrapper.py	Mon Aug 24 09:29:12 2015 +0000
@@ -0,0 +1,358 @@
+#!/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__()