Example #1
0
def convert_fasta(ref_fasta, just_name=False):
    out_fa = ref_fasta + ".bwameth.c2t"
    if just_name:
        return out_fa
    msg = "c2t in %s to %s" % (ref_fasta, out_fa)
    if is_newer_b(ref_fasta, out_fa):
        sys.stderr.write("already converted: %s\n" % msg)
        return out_fa
    sys.stderr.write("converting %s\n" % msg)
    try:
        fh = open(out_fa, "w")
        for header, seq in fasta_iter(ref_fasta):
            ########### Reverse ######################
            fh.write(">r%s\n" % header)

            #if non_cpg_only:
            #    for ctx in "TAG": # use "ATC" for fwd
            #        seq = seq.replace('G' + ctx, "A" + ctx)
            #    for line in wrap(seq):
            #        print >>fh, line
            #else:
            for line in wrap(seq.replace("G", "A")):
                fh.write(line + '\n')

            ########### Forward ######################
            fh.write(">f%s\n" % header)
            for line in wrap(seq.replace("C", "T")):
                fh.write(line + '\n')
        fh.close()
    except:
        fh.close(); os.unlink(out_fa)
        raise
    return out_fa
Example #2
0
def bwa_mem(fa,
            fq_convert_cmd,
            extra_args,
            threads=1,
            rg=None,
            paired=True,
            set_as_failed=None,
            do_not_penalize_chimeras=False):
    conv_fa = convert_fasta(fa, just_name=True)
    if not is_newer_b(conv_fa, (conv_fa + '.amb', conv_fa + '.sa')):
        raise BWAMethException("first run bwameth.py index %s" % fa)

    if not rg is None and not rg.startswith('@RG'):
        rg = '@RG\\tID:{rg}\\tSM:{rg}'.format(rg=rg)

    #starts the pipeline with the program to convert fastqs
    cmd = ("|%s " % fq_convert_cmd)

    # penalize clipping and unpaired. lower penalty on mismatches (-B)
    cmd += "|bwa mem -T 40 -B 2 -L 10 -CM "

    if paired:
        cmd += ("-U 100 -p ")
    cmd += "-R '{rg}' -t {threads} {extra_args} {conv_fa} -"
    cmd = cmd.format(**locals())
    sys.stderr.write("running: %s\n" % cmd.lstrip("|"))
    as_bam(cmd, fa, set_as_failed, do_not_penalize_chimeras)
Example #3
0
def bwa_mem(fa,
            mfq,
            extra_args,
            prefix='bwa-meth',
            threads=1,
            rg=None,
            calmd=False,
            paired=True,
            set_as_failed=None):
    conv_fa = convert_fasta(fa, just_name=True)
    if not is_newer_b(conv_fa, (conv_fa + '.amb', conv_fa + '.sa')):
        raise BWAMethException("first run bwameth.py index %s" % fa)

    if not rg is None and not rg.startswith('@RG'):
        rg = '@RG\tID:{rg}\tSM:{rg}'.format(rg=rg)

    # penalize clipping and unpaired. lower penalty on mismatches (-B)
    cmd = "|bwa mem -T 40 -B 2 -L 10 -CM "

    if paired:
        cmd += ("-U 100 -p ")
    cmd += "-R '{rg}' -t {threads} {extra_args} {conv_fa} {mfq}"
    cmd = cmd.format(**locals())
    sys.stderr.write("running: %s\n" % cmd.lstrip("|"))
    as_bam(cmd, fa, prefix, calmd, set_as_failed)
Example #4
0
def bwa_index(fa):
    if is_newer_b(fa, (fa + '.amb', fa + '.sa')):
        return
    sys.stderr.write("indexing: %s\n" % fa)
    try:
        run("bwa index -a bwtsw %s" % fa)
    except:
        if op.exists(fa + ".amb"):
            os.unlink(fa + ".amb")
        raise
Example #5
0
def bwa_index(fa):
    if is_newer_b(fa, (fa + '.amb', fa + '.sa')):
        return
    sys.stderr.write("indexing: %s\n" % fa)
    try:
        run("bwa index -a bwtsw %s" % fa)
    except:
        if op.exists(fa + ".amb"):
            os.unlink(fa + ".amb")
        raise
Example #6
0
def bwa_mem(fa, mfq, extra_args, prefix='bwa-meth', threads=1, rg=None,
            calmd=False, paired=True, set_as_failed=None):
    conv_fa = convert_fasta(fa, just_name=True)
    if not is_newer_b(conv_fa, (conv_fa + '.amb', conv_fa + '.sa')):
        raise BWAMethException("first run bwameth.py index %s" % fa)

    # penalize clipping and unpaired. lower penalty on mismatches (-B)
    cmd = "|bwa mem -T 40 -B 2 -L 10 -CM "

    if paired:
        cmd += ("-U 100 -p ")
    cmd += "-t {threads} {extra_args} {conv_fa} {mfq}"
    cmd = cmd.format(**locals())
    sys.stderr.write("running: %s\n" % cmd.lstrip("|"))
    as_bam(cmd, fa, prefix, calmd, set_as_failed)
Example #7
0
def bwa_mem(fa, mfq, extra_args, threads=1, rg=None,
            paired=True, set_as_failed=None):
    conv_fa = convert_fasta(fa, just_name=True)
    if not is_newer_b(conv_fa, (conv_fa + '.amb', conv_fa + '.sa')):
        raise BWAMethException("first run bwameth.py index %s" % fa)

    if not rg is None and not rg.startswith('@RG'):
        rg = '@RG\tID:{rg}\tSM:{rg}'.format(rg=rg)

    # penalize clipping and unpaired. lower penalty on mismatches (-B)
    cmd = "|bwa mem -T 40 -B 2 -L 10 -CM "

    if paired:
        cmd += ("-U 100 -p ")
    cmd += "-R '{rg}' -t {threads} {extra_args} {conv_fa} {mfq}"
    cmd = cmd.format(**locals())
    sys.stderr.write("running: %s\n" % cmd.lstrip("|"))
    as_bam(cmd, fa, set_as_failed)
Example #8
0
def convert_fasta(ref_fasta, just_name=False):
    out_fa = ref_fasta + ".bwameth.c2t"
    if just_name:
        return out_fa
    msg = "c2t in %s to %s" % (ref_fasta, out_fa)
    if is_newer_b(ref_fasta, out_fa):
        sys.stderr.write("already converted: %s\n" % msg)
        return out_fa
    sys.stderr.write("converting %s\n" % msg)
    try:
        fh = open(out_fa, "w")
        for header, seq in fasta_iter(ref_fasta):
            ########### Reverse ######################
            fh.write(">r%s\n" % header)

            #if non_cpg_only:
            #    for ctx in "TAG": # use "ATC" for fwd
            #        seq = seq.replace('G' + ctx, "A" + ctx)
            #    for line in wrap(seq):
            #        print >>fh, line
            #else:
            for line in wrap(seq.replace("G", "A")):
                fh.write(line + '\n')

            ########### Forward ######################
            fh.write(">f%s\n" % header)
            for line in wrap(seq.replace("C", "T")):
                fh.write(line + '\n')
        fh.close()
    except:
        try:
            fh.close()
        except UnboundLocalError:
            pass
        os.unlink(out_fa)
        raise
    return out_fa
Example #9
0
def bwa_mem(fa,
            fq_convert_cmd,
            extra_args,
            threads=1,
            minSeedLength=19,
            bandWidth=100,
            dropoff=100,
            mismatchPenalty=2,
            gapOpenPenalty=6,
            gapExtensionPenalty=1,
            clippingPenalty=10,
            minAlignmentScore=40,
            rg=None,
            paired=True,
            set_as_failed=None):
    conv_fa = convert_fasta(fa, just_name=True)
    if not is_newer_b(conv_fa, (conv_fa + '.amb', conv_fa + '.sa')):
        raise BWAMethException("first run bwameth.py index %s" % fa)

    if not rg is None and not rg.startswith('@RG'):
        rg = '@RG\\tID:{rg}\\tSM:{rg}'.format(rg=rg)

    #starts the pipeline with the program to convert fastqs
    cmd = ("|%s " % fq_convert_cmd)

    # penalize clipping and unpaired. lower penalty on mismatches (-B)
    cmd += "|bwa mem -CM "

    if paired:
        cmd += ("-U 100 -p ")
    cmd += f"-R '{rg}' -t {threads} -k {minSeedLength} -w {bandWidth} -d {dropoff} "
    cmd += f"-B {mismatchPenalty} -O {gapOpenPenalty} -E {gapExtensionPenalty} "
    cmd += f"-L {clippingPenalty} -T {minAlignmentScore}  {extra_args} {conv_fa} -"
    #cmd = cmd.format(**locals())

    sys.stderr.write("running: %s\n" % cmd.lstrip("|"))
    as_bam(cmd, fa, set_as_failed)