def align_and_count_hits(inBam, refFasta, outCounts, includeZeros=False, JVMmemory=None): ''' Take reads, align to reference with Novoalign and return aligned read counts for each reference sequence. ''' bam_aligned = mkstempfname('.aligned.bam') tools.novoalign.NovoalignTool().execute(inBam, refFasta, bam_aligned, options=['-r', 'Random'], JVMmemory=JVMmemory) samtools = tools.samtools.SamtoolsTool() seqs = list( dict(x.split(':', 1) for x in row[1:])['SN'] for row in samtools.getHeader(bam_aligned) if row[0] == '@SQ') with util.file.open_or_gzopen(outCounts, 'w') as outf: for seq in seqs: n = samtools.count(bam_aligned, regions=[seq]) if n > 0 or includeZeros: outf.write("{}\t{}\n".format(seq, n)) os.unlink(bam_aligned)
def align_and_count_hits(inBam, refFasta, outCounts, includeZeros=False, JVMmemory=None, threads=1): ''' Take reads, align to reference with Novoalign and return aligned read counts for each reference sequence. ''' bam_aligned = mkstempfname('.aligned.bam') tools.novoalign.NovoalignTool().execute( inBam, refFasta, bam_aligned, options=['-r', 'Random'], JVMmemory=JVMmemory) samtools = tools.samtools.SamtoolsTool() seqs = list(dict(x.split(':', 1) for x in row[1:])['SN'] for row in samtools.getHeader(bam_aligned) if row[0]=='@SQ') with util.file.open_or_gzopen(outCounts, 'w') as outf: for seq in seqs: n = samtools.count(bam_aligned, regions=[seq]) if n>0 or includeZeros: outf.write("{}\t{}\n".format(seq, n)) os.unlink(bam_aligned)
def split_bam(inBam, outBams): '''Split BAM file equally into several output BAM files. ''' samtools = tools.samtools.SamtoolsTool() picard = tools.picard.PicardTools() # get totalReadCount and maxReads # maxReads = totalReadCount / num files, but round up to the nearest # even number in order to keep read pairs together (assuming the input # is sorted in query order and has no unmated reads, which can be # accomplished by Picard RevertSam with SANITIZE=true) totalReadCount = samtools.count(inBam) maxReads = int(math.ceil(float(totalReadCount) / len(outBams) / 2) * 2) log.info("splitting %d reads into %d files of %d reads each", totalReadCount, len(outBams), maxReads) # load BAM header into memory header = samtools.getHeader(inBam) if 'SO:queryname' not in header[0]: raise Exception('Input BAM file must be sorted in queryame order') # dump to bigsam bigsam = mkstempfname('.sam') samtools.view([], inBam, bigsam) # split bigsam into little ones with util.file.open_or_gzopen(bigsam, 'rt') as inf: for outBam in outBams: log.info("preparing file " + outBam) tmp_sam_reads = mkstempfname('.sam') with open(tmp_sam_reads, 'wt') as outf: for row in header: outf.write('\t'.join(row) + '\n') for _ in range(maxReads): line = inf.readline() if not line: break outf.write(line) if outBam == outBams[-1]: for line in inf: outf.write(line) picard.execute("SamFormatConverter", [ 'INPUT=' + tmp_sam_reads, 'OUTPUT=' + outBam, 'VERBOSITY=WARNING' ], JVMmemory='512m') os.unlink(tmp_sam_reads) os.unlink(bigsam)
def split_bam(inBam, outBams): '''Split BAM file equally into several output BAM files. ''' samtools = tools.samtools.SamtoolsTool() picard = tools.picard.PicardTools() # get totalReadCount and maxReads # maxReads = totalReadCount / num files, but round up to the nearest # even number in order to keep read pairs together (assuming the input # is sorted in query order and has no unmated reads, which can be # accomplished by Picard RevertSam with SANITIZE=true) totalReadCount = samtools.count(inBam) maxReads = int(math.ceil(float(totalReadCount) / len(outBams) / 2) * 2) log.info("splitting %d reads into %d files of %d reads each", totalReadCount, len(outBams), maxReads) # load BAM header into memory header = samtools.getHeader(inBam) if 'SO:queryname' not in header[0]: raise Exception('Input BAM file must be sorted in queryame order') # dump to bigsam bigsam = mkstempfname('.sam') samtools.view([], inBam, bigsam) # split bigsam into little ones with util.file.open_or_gzopen(bigsam, 'rt') as inf: for outBam in outBams: log.info("preparing file " + outBam) tmp_sam_reads = mkstempfname('.sam') with open(tmp_sam_reads, 'wt') as outf: for row in header: outf.write('\t'.join(row) + '\n') for _ in range(maxReads): line = inf.readline() if not line: break outf.write(line) if outBam == outBams[-1]: for line in inf: outf.write(line) picard.execute( "SamFormatConverter", [ 'INPUT=' + tmp_sam_reads, 'OUTPUT=' + outBam, 'VERBOSITY=WARNING' ], JVMmemory='512m' ) os.unlink(tmp_sam_reads) os.unlink(bigsam)
def align_one_rg_bam(self, inBam, refFasta, outBam, rgid=None, rgs=None, options=None, min_qual=0, JVMmemory=None): ''' Execute Novoalign on BAM inputs and outputs. Requires that only one RG exists (will error otherwise). Use Picard to sort and index the output BAM. If min_qual>0, use Samtools to filter on mapping quality. ''' options = options or ["-r", "Random"] samtools = tools.samtools.SamtoolsTool() # Require exactly one RG rgs = rgs if rgs is not None else samtools.getReadGroups(inBam) if len(rgs) == 0: raise InvalidBamHeaderError("{} lacks read groups".format(inBam)) elif len(rgs) == 1: if not rgid: rgid = list(rgs.keys())[0] elif not rgid: raise InvalidBamHeaderError("{} has {} read groups, but we require exactly one".format(inBam, len(rgs))) if rgid not in rgs: raise InvalidBamHeaderError("{} has read groups, but not {}".format(inBam, rgid)) #rg = rgs[rgid] # Strip inBam to just one RG (if necessary) if len(rgs) == 1: one_rg_inBam = inBam else: # strip inBam to one read group tmp_bam = util.file.mkstempfname('.onebam.bam') samtools.view(['-b', '-r', rgid], inBam, tmp_bam) # special exit if this file is empty if samtools.count(tmp_bam) == 0: return # simplify BAM header otherwise Novoalign gets confused one_rg_inBam = util.file.mkstempfname('.{}.in.bam'.format(rgid)) headerFile = util.file.mkstempfname('.{}.header.txt'.format(rgid)) with open(headerFile, 'wt') as outf: for row in samtools.getHeader(inBam): if len(row) > 0 and row[0] == '@RG': if rgid != list(x[3:] for x in row if x.startswith('ID:'))[0]: # skip all read groups that are not rgid continue outf.write('\t'.join(row) + '\n') samtools.reheader(tmp_bam, headerFile, one_rg_inBam) os.unlink(tmp_bam) os.unlink(headerFile) # Novoalign tmp_sam = util.file.mkstempfname('.novoalign.sam') tmp_sam_err = util.file.mkstempfname('.novoalign.sam.err') cmd = [self.install_and_get_path(), '-f', one_rg_inBam] + list(map(str, options)) cmd = cmd + ['-F', 'BAM', '-d', self._fasta_to_idx_name(refFasta), '-o', 'SAM'] _log.debug(' '.join(cmd)) with open(tmp_sam, 'wt') as outf: util.misc.run_and_save(cmd, outf=outf) # Samtools filter (optional) if min_qual: tmp_bam2 = util.file.mkstempfname('.filtered.bam') cmd = [samtools.install_and_get_path(), 'view', '-b', '-S', '-1', '-q', str(min_qual), tmp_sam] _log.debug('%s > %s', ' '.join(cmd), tmp_bam2) with open(tmp_bam2, 'wb') as outf: util.misc.run_and_save(cmd, outf=outf) os.unlink(tmp_sam) tmp_sam = tmp_bam2 # Picard SortSam sorter = tools.picard.SortSamTool() sorter.execute( tmp_sam, outBam, sort_order='coordinate', picardOptions=['CREATE_INDEX=true', 'VALIDATION_STRINGENCY=SILENT'], JVMmemory=JVMmemory )
def align_mem_one_rg(self, inBam, refDb, outBam, rgid=None, options=None, min_score_to_filter=None, threads=None, JVMmemory=None, invert_filter=False, should_index=True): """ Performs an alignment of one read group in a bam file to a reference fasta file TODO: With the addition of a third aligner to viral-ngs, the functionality common to this method and to the comparable method in the Novoalign wrapper should be broken out as an "aligner" superclass, capable of aligning bam or fastq files with an arbitrary aligner, while preserving read groups. """ options = options or [] samtools = tools.samtools.SamtoolsTool() # Require exactly one RG rgs = samtools.getReadGroups(inBam) if len(rgs) == 0: raise InvalidBamHeaderError("{} lacks read groups".format(inBam)) elif len(rgs) == 1: if not rgid: rgid = list(rgs.keys())[0] elif not rgid: raise InvalidBamHeaderError( "{} has {} read groups, but we require exactly one".format( inBam, len(rgs))) if rgid not in rgs: raise InvalidBamHeaderError( "{} has read groups, but not {}".format(inBam, rgid)) headerFile = util.file.mkstempfname('.{}.header.txt'.format(rgid)) # Strip inBam to just one RG (if necessary) removeInput = False if len(rgs) == 1: one_rg_inBam = inBam tools.samtools.SamtoolsTool().dumpHeader(one_rg_inBam, headerFile) else: # strip inBam to one read group with util.file.tempfname('.onebam.bam') as tmp_bam: samtools.view(['-b', '-r', rgid], inBam, tmp_bam) # special exit if this file is empty if samtools.count(tmp_bam) == 0: log.warning("No reads present for RG %s in file: %s", rgid, inBam) return # simplify BAM header otherwise Novoalign gets confused one_rg_inBam = util.file.mkstempfname( '.{}.in.bam'.format(rgid)) removeInput = True with open(headerFile, 'wt') as outf: for row in samtools.getHeader(inBam): if len(row) > 0 and row[0] == '@RG': if rgid != list(x[3:] for x in row if x.startswith('ID:'))[0]: # skip all read groups that are not rgid continue outf.write('\t'.join(row) + '\n') samtools.reheader(tmp_bam, headerFile, one_rg_inBam) # perform actual alignment # get the read group line to give to BWA readgroup_line = "" with open(headerFile) as inf: for line in inf: if line.startswith("@RG"): readgroup_line = line assert len(readgroup_line) > 0 #with util.file.tempfname('.aligned.bam') as tmp_bam_aligned: # rather than reheader the alignment bam file later so it has the readgroup information # from the original bam file, we'll pass the RG line to bwa to write out self.mem( one_rg_inBam, refDb, outBam, options=options + ['-R', readgroup_line.rstrip("\r\n").replace('\t', '\\t')], min_score_to_filter=min_score_to_filter, threads=threads, invert_filter=invert_filter, should_index=should_index) return (rgid, outBam) # if there was more than one RG in the input, we had to create a temporary file with the one RG specified # and we can safely delete it this file # if there was only one RG in the input, we used it directly and should not delete it if removeInput: os.unlink(one_rg_inBam)
def align_mem_one_rg(self, inBam, refDb, outBam, rgid=None, options=None, min_score_to_filter=None, threads=None, JVMmemory=None): """ Performs an alignment of one read group in a bam file to a reference fasta file TODO: With the addition of a third aligner to viral-ngs, the functionality common to this method and to the comparable method in the Novoalign wrapper should be broken out as an "aligner" superclass, capable of aligning bam or fastq files with an arbitrary aligner, while preserving read groups. """ options = options or [] samtools = tools.samtools.SamtoolsTool() # Require exactly one RG rgs = samtools.getReadGroups(inBam) if len(rgs) == 0: raise InvalidBamHeaderError("{} lacks read groups".format(inBam)) elif len(rgs) == 1: if not rgid: rgid = list(rgs.keys())[0] elif not rgid: raise InvalidBamHeaderError("{} has {} read groups, but we require exactly one".format(inBam, len(rgs))) if rgid not in rgs: raise InvalidBamHeaderError("{} has read groups, but not {}".format(inBam, rgid)) headerFile = util.file.mkstempfname('.{}.header.txt'.format(rgid)) # Strip inBam to just one RG (if necessary) removeInput = False if len(rgs) == 1: one_rg_inBam = inBam tools.samtools.SamtoolsTool().dumpHeader(one_rg_inBam, headerFile) else: # strip inBam to one read group tmp_bam = util.file.mkstempfname('.onebam.bam') samtools.view(['-b', '-r', rgid], inBam, tmp_bam) # special exit if this file is empty if samtools.count(tmp_bam) == 0: log.warning("No reads present for RG %s in file: %s", rgid, inBam) return # simplify BAM header otherwise Novoalign gets confused one_rg_inBam = util.file.mkstempfname('.{}.in.bam'.format(rgid)) removeInput = True with open(headerFile, 'wt') as outf: for row in samtools.getHeader(inBam): if len(row) > 0 and row[0] == '@RG': if rgid != list(x[3:] for x in row if x.startswith('ID:'))[0]: # skip all read groups that are not rgid continue outf.write('\t'.join(row) + '\n') samtools.reheader(tmp_bam, headerFile, one_rg_inBam) os.unlink(tmp_bam) # perform actual alignment # get the read group line to give to BWA readgroup_line = "" with open(headerFile) as inf: for line in inf: if line.startswith("@RG"): readgroup_line = line assert len(readgroup_line) > 0 tmp_bam_aligned = util.file.mkstempfname('.aligned.bam') # rather than reheader the alignment bam file later so it has the readgroup information # from the original bam file, we'll pass the RG line to bwa to write out self.mem(one_rg_inBam, refDb, tmp_bam_aligned, options=options+['-R', readgroup_line.rstrip("\r\n")], min_score_to_filter=min_score_to_filter, threads=threads) # if there was more than one RG in the input, we had to create a temporary file with the one RG specified # and we can safely delete it this file # if there was only one RG in the input, we used it directly and should not delete it if removeInput: os.unlink(one_rg_inBam) # if the aligned bam file contains no reads after filtering # just create an empty file if tools.samtools.SamtoolsTool().count(tmp_bam_aligned) == 0: util.file.touch(outBam) else: # samtools reheader seems to segfault on some alignments created by bwa # so rather than reheader, BWA will write out the RG given to it via '-R' # reheadered_bam = util.file.mkstempfname('.reheadered.bam') # tools.samtools.SamtoolsTool().reheader(tmp_bam_aligned, headerFile, reheadered_bam) # os.unlink(tmp_bam_aligned) # os.unlink(headerFile) # os.system("samtools view -h {} > /Users/tomkinsc/Desktop/test_reheader.bam".format(reheadered_bam)) # sort sorter = tools.picard.SortSamTool() sorter.execute( tmp_bam_aligned, outBam, sort_order='coordinate', picardOptions=['CREATE_INDEX=true', 'VALIDATION_STRINGENCY=SILENT'], JVMmemory=JVMmemory )
def align_mem_one_rg(self, inBam, refDb, outBam, rgid=None, options=None, min_qual=30, threads=None, JVMmemory=None): """ Performs an alignment of one read group in a bam file to a reference fasta file TODO: With the addition of a third aligner to viral-ngs, the functionality common to this method and to the comparable method in the Novoalign wrapper should be broken out as an "aligner" superclass, capable of aligning bam or fastq files with an arbitrary aligner, while preserving read groups. """ options = options or [] samtools = tools.samtools.SamtoolsTool() # Require exactly one RG rgs = samtools.getReadGroups(inBam) if len(rgs) == 0: raise InvalidBamHeaderError("{} lacks read groups".format(inBam)) elif len(rgs) == 1: if not rgid: rgid = list(rgs.keys())[0] elif not rgid: raise InvalidBamHeaderError("{} has {} read groups, but we require exactly one".format(inBam, len(rgs))) if rgid not in rgs: raise InvalidBamHeaderError("{} has read groups, but not {}".format(inBam, rgid)) headerFile = util.file.mkstempfname('.{}.header.txt'.format(rgid)) # Strip inBam to just one RG (if necessary) removeInput = False if len(rgs) == 1: one_rg_inBam = inBam tools.samtools.SamtoolsTool().dumpHeader(one_rg_inBam, headerFile) else: # strip inBam to one read group tmp_bam = util.file.mkstempfname('.onebam.bam') samtools.view(['-b', '-r', rgid], inBam, tmp_bam) # special exit if this file is empty if samtools.count(tmp_bam) == 0: return # simplify BAM header otherwise Novoalign gets confused one_rg_inBam = util.file.mkstempfname('.{}.in.bam'.format(rgid)) removeInput = True with open(headerFile, 'wt') as outf: for row in samtools.getHeader(inBam): if len(row) > 0 and row[0] == '@RG': if rgid != list(x[3:] for x in row if x.startswith('ID:'))[0]: # skip all read groups that are not rgid continue outf.write('\t'.join(row) + '\n') samtools.reheader(tmp_bam, headerFile, one_rg_inBam) os.unlink(tmp_bam) # perform actual alignment # get the read group line to give to BWA readgroup_line = "" with open(headerFile) as inf: for line in inf: if line.startswith("@RG"): readgroup_line = line assert len(readgroup_line) > 0 aln_bam_prefilter = util.file.mkstempfname('.prefiltered.bam') # rather than reheader the alignment bam file later so it has the readgroup information # from the original bam file, we'll pass the RG line to bwa to write out self.mem(one_rg_inBam, refDb, aln_bam_prefilter, options=options+['-R', readgroup_line.rstrip("\n").rstrip("\r")], min_qual=min_qual, threads=threads) # if there was more than one RG in the input, we had to create a temporary file with the one RG specified # and we can safely delete it this file # if there was only one RG in the input, we used it directly and should not delete it if removeInput: os.unlink(one_rg_inBam) # @haydenm says: # For some reason (particularly when the --sensitive option is on), bwa # doesn't listen to its '-T' flag and outputs alignments with score less # than the '-T 30' threshold. So filter these: if min_qual > 0: tmp_bam_aligned = util.file.mkstempfname('.aligned.bam') tools.samtools.SamtoolsTool().view(["-b", "-h", "-q", str(min_qual)], aln_bam_prefilter, tmp_bam_aligned) os.unlink(aln_bam_prefilter) else: shutil.move(aln_bam_prefilter, tmp_bam_aligned) # if the aligned bam file contains no reads after filtering # just create an empty file if tools.samtools.SamtoolsTool().count(tmp_bam_aligned) == 0: util.file.touch(outBam) else: # samtools reheader seems to segfault on some alignments created by bwa # so rather than reheader, BWA will write out the RG given to it via '-R' # reheadered_bam = util.file.mkstempfname('.reheadered.bam') # tools.samtools.SamtoolsTool().reheader(tmp_bam_aligned, headerFile, reheadered_bam) # os.unlink(tmp_bam_aligned) # os.unlink(headerFile) # os.system("samtools view -h {} > /Users/tomkinsc/Desktop/test_reheader.bam".format(reheadered_bam)) # sort sorter = tools.picard.SortSamTool() sorter.execute( tmp_bam_aligned, outBam, sort_order='coordinate', picardOptions=['CREATE_INDEX=true', 'VALIDATION_STRINGENCY=SILENT'], JVMmemory=JVMmemory )
def align_one_rg(self, inBam, refDb, outBam, rgid=None, preset=None, options=None, threads=None, JVMmemory=None): """ Performs an alignment of one read group in a bam file to a reference fasta file using minimap2. Emits alignments in sorted, index bam files. inBam may contain more read groups, but we will subset input to the specified rgid. preset may be specified as a valid value for "minimap2 -x" which depends on the type of data (short accurate reads vs long noisy reads). If preset is set to None, we will autodetect based on the PL (platform) tag in the read group header (e.g. illumina, ont, pacbio) """ options = list(options).copy() or [] samtools = tools.samtools.SamtoolsTool() # Require exactly one RG rgs = samtools.getReadGroups(inBam) if len(rgs) == 0: raise InvalidBamHeaderError("{} lacks read groups".format(inBam)) elif len(rgs) == 1: if not rgid: rgid = list(rgs.keys())[0] elif not rgid: raise InvalidBamHeaderError("{} has {} read groups, but we require exactly one".format(inBam, len(rgs))) if rgid not in rgs: raise InvalidBamHeaderError("{} has read groups, but not {}".format(inBam, rgid)) headerFile = util.file.mkstempfname('.{}.header.txt'.format(rgid)) # Strip inBam to just one RG (if necessary) removeInput = False if len(rgs) == 1: one_rg_inBam = inBam tools.samtools.SamtoolsTool().dumpHeader(one_rg_inBam, headerFile) else: # strip inBam to one read group with util.file.tempfname('.onebam.bam') as tmp_bam: samtools.view(['-1', '-r', rgid], inBam, tmp_bam) # special exit if this file is empty if samtools.isEmpty(tmp_bam): log.warning("No reads present for RG %s in file: %s", rgid, inBam) shutil.copyfile(tmp_bam, outBam) return # simplify BAM header otherwise Novoalign gets confused one_rg_inBam = util.file.mkstempfname('.{}.in.bam'.format(rgid)) removeInput = True with open(headerFile, 'wt') as outf: for row in samtools.getHeader(inBam): if len(row) > 0 and row[0] == '@RG': if rgid != list(x[3:] for x in row if x.startswith('ID:'))[0]: # skip all read groups that are not rgid continue outf.write('\t'.join(row) + '\n') samtools.reheader(tmp_bam, headerFile, one_rg_inBam) # get the read group line to give to mm2 readgroup_line = "" with open(headerFile) as inf: for line in inf: if line.startswith("@RG"): readgroup_line = line.rstrip("\r\n") if not readgroup_line: raise Exception() # rather than reheader the alignment bam file later so it has the readgroup information # from the original bam file, we'll pass the RG line to minimap2 to write out options.extend(('-R', readgroup_line.replace('\t','\\t'))) # dynamically determine the mode of operation if '-x' not in options: if preset is None: platform = list(x for x in readgroup_line.split('\t') if x.startswith('PL:')) if len(platform) != 1: raise Exception("cannot autodetect minimap2 aligner mode when PL: tag is not set in the read group header for {}: {}".format(inBam, readgroup_line)) else: platform = platform[0][3:].lower() if platform == 'illumina': preset = 'sr' elif platform == 'ont': preset = 'map-ont' elif platform == 'pacbio': preset = 'map-pb' else: raise Exception("PL: tag {} for read group {} in bam {} refers to a data type we do not know how to map with minimap2".format(platform, rgid, inBam)) options.extend(('-x', preset)) # perform actual alignment if samtools.isEmpty(one_rg_inBam): # minimap doesn't like empty inputs, so copy empty bam through samtools.sort(one_rg_inBam, outBam) else: self.align_cmd(one_rg_inBam, refDb, outBam, options=options, threads=threads) # if there was more than one RG in the input, we had to create a temporary file with the one RG specified # and we can safely delete it this file # if there was only one RG in the input, we used it directly and should not delete it if removeInput: os.unlink(one_rg_inBam)
def align_mem_one_rg(self, inBam, refDb, outBam, rgid=None, options=None, min_score_to_filter=None, threads=None, JVMmemory=None, invert_filter=False, should_index=True): """ Performs an alignment of one read group in a bam file to a reference fasta file TODO: With the addition of a third aligner to viral-ngs, the functionality common to this method and to the comparable method in the Novoalign wrapper should be broken out as an "aligner" superclass, capable of aligning bam or fastq files with an arbitrary aligner, while preserving read groups. """ options = options or [] samtools = tools.samtools.SamtoolsTool() # Require exactly one RG rgs = samtools.getReadGroups(inBam) if len(rgs) == 0: raise InvalidBamHeaderError("{} lacks read groups".format(inBam)) elif len(rgs) == 1: if not rgid: rgid = list(rgs.keys())[0] elif not rgid: raise InvalidBamHeaderError("{} has {} read groups, but we require exactly one".format(inBam, len(rgs))) if rgid not in rgs: raise InvalidBamHeaderError("{} has read groups, but not {}".format(inBam, rgid)) headerFile = util.file.mkstempfname('.{}.header.txt'.format(rgid)) # Strip inBam to just one RG (if necessary) removeInput = False if len(rgs) == 1: one_rg_inBam = inBam tools.samtools.SamtoolsTool().dumpHeader(one_rg_inBam, headerFile) else: # strip inBam to one read group with util.file.tempfname('.onebam.bam') as tmp_bam: samtools.view(['-b', '-r', rgid], inBam, tmp_bam) # special exit if this file is empty if samtools.count(tmp_bam) == 0: log.warning("No reads present for RG %s in file: %s", rgid, inBam) return # simplify BAM header otherwise Novoalign gets confused one_rg_inBam = util.file.mkstempfname('.{}.in.bam'.format(rgid)) removeInput = True with open(headerFile, 'wt') as outf: for row in samtools.getHeader(inBam): if len(row) > 0 and row[0] == '@RG': if rgid != list(x[3:] for x in row if x.startswith('ID:'))[0]: # skip all read groups that are not rgid continue outf.write('\t'.join(row) + '\n') samtools.reheader(tmp_bam, headerFile, one_rg_inBam) # perform actual alignment # get the read group line to give to BWA readgroup_line = "" with open(headerFile) as inf: for line in inf: if line.startswith("@RG"): readgroup_line = line assert len(readgroup_line) > 0 #with util.file.tempfname('.aligned.bam') as tmp_bam_aligned: # rather than reheader the alignment bam file later so it has the readgroup information # from the original bam file, we'll pass the RG line to bwa to write out self.mem(one_rg_inBam, refDb, outBam, options=options+['-R', readgroup_line.rstrip("\r\n").replace('\t','\\t')], min_score_to_filter=min_score_to_filter, threads=threads, invert_filter=invert_filter, should_index=should_index) return (rgid, outBam) # if there was more than one RG in the input, we had to create a temporary file with the one RG specified # and we can safely delete it this file # if there was only one RG in the input, we used it directly and should not delete it if removeInput: os.unlink(one_rg_inBam)