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