def parser_deplete_bwa_bam(parser=argparse.ArgumentParser()):
parser.add_argument('inBam', help='Input BAM file.')
parser.add_argument('refDbs', nargs='+', help='One or more reference databases for bwa. '
'An ephemeral database will be created if a fasta file is provided.')
parser.add_argument('outBam', help='Ouput BAM file with matching reads removed.')
parser = read_utils.parser_revert_sam_common(parser)
util.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))
util.cmd.attach_main(parser, main_deplete_bwa_bam)
return parser
def parser_deplete(parser=argparse.ArgumentParser()):
parser.add_argument('inBam', help='Input BAM file.')
parser.add_argument('revertBam',
nargs='?',
help='Output BAM: read markup reverted with Picard.')
parser.add_argument('bwaBam',
help='Output BAM: depleted of reads with BWA.')
parser.add_argument('bmtaggerBam',
help='Output BAM: depleted of reads with BMTagger.')
parser.add_argument(
'rmdupBam',
help='Output BAM: bmtaggerBam run through M-Vicuna duplicate removal.')
parser.add_argument(
'blastnBam',
help=
'Output BAM: rmdupBam run through another depletion of reads with BLASTN.'
)
parser.add_argument(
'--bwaDbs',
nargs='*',
default=(),
help='Reference databases for blast to deplete from input.')
parser.add_argument('--bmtaggerDbs',
nargs='*',
default=(),
help='''Reference databases to deplete from input.
For each db, requires prior creation of db.bitmask by bmtool,
and db.srprism.idx, db.srprism.map, etc. by srprism mkindex.'''
)
parser.add_argument(
'--blastDbs',
nargs='*',
default=(),
help='Reference databases for blast to deplete from input.')
parser.add_argument('--srprismMemory',
dest="srprism_memory",
type=int,
default=7168,
help='Memory for srprism.')
parser.add_argument("--chunkSize",
type=int,
default=1000000,
help='blastn chunk size (default: %(default)s)')
parser.add_argument(
'--JVMmemory',
default=tools.picard.FilterSamReadsTool.jvmMemDefault,
help=
'JVM virtual memory size for Picard FilterSamReads (default: %(default)s)'
)
parser = read_utils.parser_revert_sam_common(parser)
util.cmd.common_args(parser, (('threads', None), ('loglevel', None),
('version', None), ('tmp_dir', None)))
util.cmd.attach_main(parser, main_deplete)
return parser
def parser_deplete_blastn_bam(parser=argparse.ArgumentParser()):
parser.add_argument('inBam', help='Input BAM file.')
parser.add_argument('refDbs', nargs='+', help='One or more reference databases for blast. '
'An ephemeral database will be created if a fasta file is provided.')
parser.add_argument('outBam', help='Output BAM file with matching reads removed.')
parser.add_argument("--chunkSize", type=int, default=1000000, help='FASTA chunk size (default: %(default)s)')
parser.add_argument(
'--JVMmemory',
default=tools.picard.FilterSamReadsTool.jvmMemDefault,
help='JVM virtual memory size (default: %(default)s)'
)
parser = read_utils.parser_revert_sam_common(parser)
util.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))
util.cmd.attach_main(parser, main_deplete_blastn_bam)
return parser
def parser_deplete_bam_bmtagger(parser=argparse.ArgumentParser()):
parser.add_argument('inBam', help='Input BAM file.')
parser.add_argument(
'refDbs',
nargs='+',
help='''Reference databases (one or more) to deplete from input.
For each db, requires prior creation of db.bitmask by bmtool,
and db.srprism.idx, db.srprism.map, etc. by srprism mkindex.'''
)
parser.add_argument('outBam', help='Output BAM file.')
parser.add_argument('--srprismMemory', dest="srprism_memory", type=int, default=7168, help='Memory for srprism.')
parser.add_argument(
'--JVMmemory',
default=tools.picard.FilterSamReadsTool.jvmMemDefault,
help='JVM virtual memory size (default: %(default)s)'
)
parser = read_utils.parser_revert_sam_common(parser)
util.cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))
util.cmd.attach_main(parser, main_deplete_bam_bmtagger)
return parser
def parser_deplete(parser=argparse.ArgumentParser()):
parser.add_argument('inBam', help='Input BAM file.')
parser.add_argument('revertBam', nargs='?', help='Output BAM: read markup reverted with Picard.')
parser.add_argument('bwaBam', help='Output BAM: depleted of reads with BWA.')
parser.add_argument('bmtaggerBam', help='Output BAM: depleted of reads with BMTagger.')
parser.add_argument('rmdupBam', help='Output BAM: bmtaggerBam run through M-Vicuna duplicate removal.')
parser.add_argument(
'blastnBam', help='Output BAM: rmdupBam run through another depletion of reads with BLASTN.'
)
parser.add_argument(
'--bwaDbs',
nargs='*',
default=(),
help='Reference databases for blast to deplete from input.'
)
parser.add_argument(
'--bmtaggerDbs',
nargs='*',
default=(),
help='''Reference databases to deplete from input.
For each db, requires prior creation of db.bitmask by bmtool,
and db.srprism.idx, db.srprism.map, etc. by srprism mkindex.'''
)
parser.add_argument(
'--blastDbs',
nargs='*',
default=(),
help='Reference databases for blast to deplete from input.'
)
parser.add_argument('--srprismMemory', dest="srprism_memory", type=int, default=7168, help='Memory for srprism.')
parser.add_argument("--chunkSize", type=int, default=1000000, help='blastn chunk size (default: %(default)s)')
parser.add_argument(
'--JVMmemory',
default=tools.picard.FilterSamReadsTool.jvmMemDefault,
help='JVM virtual memory size for Picard FilterSamReads (default: %(default)s)'
)
parser = read_utils.parser_revert_sam_common(parser)
util.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))
util.cmd.attach_main(parser, main_deplete)
return parser
