def register_args(main_func):
subparser = add_subcommand('example_subcommand', main_func, help='run example_subcommand')
# The "-1" argument below is only for this subcommand (and other subcommands
# that expressly define it). If you wish to expose it for every subcommand,
# define it under argparser._add_shared_subcommand_args.
subparser.add_argument('-1',
'--one',
action='store_const',
const=1,
dest='test_value',
help="set test_value to 1")
return main_func
def register_args(main_func):
subparser = add_subcommand(
'aws_batch_submit',
main_func,
help=
f"submit command to run under AWS Batch, keeping records under {opsdir}"
)
subparser.add_argument(
'--batch_command',
dest='batch_command',
required=False,
help="Command to run in AWS Batch container after installing iggtools")
subparser.set_defaults(batch_command="iggtools --help")
return main_func
def register_args(main_func):
subparser = add_subcommand('annotate_genes',
main_func,
help='annotate selected genomes with prokka')
subparser.add_argument(
'--genomes',
dest='genomes',
required=False,
help=
"genome[,genome...] to import; alternatively, slice in format idx:modulus, e.g. 1:30, meaning annotate genomes whose ids are 1 mod 30; or, the special keyword 'all' meaning all genomes"
)
subparser.add_argument(
'--zzz_slave_toc', dest='zzz_slave_toc', required=False, help=SUPPRESS
) # "reserved to pass table of contents from master to slave"
return main_func
def register_args(main_func):
subparser = add_subcommand('build_marker_genes', main_func, help='identify marker genes for given genomes')
subparser.add_argument('--genomes',
dest='genomes',
required=False,
help="genome[,genome...] to import; alternatively, slice in format idx:modulus, e.g. 1:30, meaning import genomes whose ids are 1 mod 30; or, the special keyword 'all' meaning all genomes")
subparser.add_argument('--zzz_slave_toc',
dest='zzz_slave_toc',
required=False,
help=SUPPRESS) # "reserved to pass table of contents from master to slave"
subparser.add_argument('--zzz_slave_marker_genes_hmm',
dest='zzz_slave_marker_genes_hmm',
required=False,
help=SUPPRESS) # "reserved to common database from master to slave"
return main_func
def register_args(main_func):
subparser = add_subcommand('build_pangenome',
main_func,
help='build pangenome for specified species')
subparser.add_argument(
'-s',
'--species',
dest='species',
required=False,
help=
"species[,species...] whose pangenome(s) to build; alternatively, species slice in format idx:modulus, e.g. 1:30, meaning build species whose ids are 1 mod 30; or, the special keyword 'all' meaning all species"
)
subparser.add_argument(
'--zzz_slave_toc', dest='zzz_slave_toc', required=False, help=SUPPRESS
) # "reserved to pass table of contents from master to slave"
return main_func
def register_args(main_func):
subparser = add_subcommand('midas_run_species', main_func, help='compute species abundance profile for given sample(s)')
subparser.add_argument('outdir',
type=str,
help="""Path to directory to store results. Name should correspond to unique sample identifier.""")
subparser.add_argument('-1',
dest='r1',
required=True,
help="FASTA/FASTQ file containing 1st mate if using paired-end reads. Otherwise FASTA/FASTQ containing unpaired reads.")
subparser.add_argument('-2',
dest='r2',
help="FASTA/FASTQ file containing 2nd mate if using paired-end reads.")
subparser.add_argument('--word_size',
dest='word_size',
default=DEFAULT_WORD_SIZE,
type=int,
metavar="INT",
help=f"Word size for BLAST search ({DEFAULT_WORD_SIZE}). Use word sizes > 16 for greatest efficiency.")
subparser.add_argument('--aln_mapid',
dest='aln_mapid',
type=float,
metavar="FLOAT",
help=f"Discard reads with alignment identity < ALN_MAPID. Values between 0-100 accepted. By default gene-specific species-level cutoffs are used, as specifeid in {params.inputs.marker_genes_hmm_cutoffs}")
subparser.add_argument('--aln_cov',
dest='aln_cov',
default=DEFAULT_ALN_COV,
type=float,
metavar="FLOAT",
help=f"Discard reads with alignment coverage < ALN_COV ({DEFAULT_ALN_COV}). Values between 0-1 accepted.")
subparser.add_argument('--max_reads',
dest='max_reads',
type=int,
metavar="INT",
help=f"Number of reads to use from input file(s). (All)")
if False:
# This is not currently in use.
subparser.add_argument('--read_length',
dest='read_length',
type=int,
metavar="INT",
help=f"Trim reads to READ_LENGTH and discard reads with length < READ_LENGTH. By default, reads are not trimmed or filtered")
return main_func
def register_args(main_func):
add_subcommand('init',
main_func,
help=f"initialize target {outputs.genomes}",
epilog=init.__doc__)
return main_func
def register_args(main_func):
subparser = add_subcommand(
'midas_run_snps',
main_func,
help='single-nucleotide-polymorphism prediction')
subparser.add_argument(
'outdir',
type=str,
help=
"""Path to directory to store results. Name should correspond to unique sample identifier."""
)
subparser.add_argument(
'-1',
dest='r1',
required=True,
help=
"FASTA/FASTQ file containing 1st mate if using paired-end reads. Otherwise FASTA/FASTQ containing unpaired reads."
)
subparser.add_argument(
'-2',
dest='r2',
help="FASTA/FASTQ file containing 2nd mate if using paired-end reads.")
subparser.add_argument(
'--max_reads',
dest='max_reads',
type=int,
metavar="INT",
help=f"Number of reads to use from input file(s). (All)")
subparser.add_argument(
'--species_cov',
type=float,
dest='species_cov',
metavar='FLOAT',
default=DEFAULT_SPECIES_COVERAGE,
help=f"Include species with >X coverage ({DEFAULT_SPECIES_COVERAGE})")
if False:
# This is unused.
subparser.add_argument('--species_topn',
type=int,
dest='species_topn',
metavar='INT',
help='Include top N most abundant species')
# Alignment flags
subparser.add_argument(
'--aln_speed',
type=str,
dest='aln_speed',
default='very-sensitive',
choices=['very-fast', 'fast', 'sensitive', 'very-sensitive'],
help=
'Alignment speed/sensitivity (very-sensitive). If aln_mode is local (default) this automatically issues the corresponding very-sensitive-local, etc flag to bowtie2.'
)
subparser.add_argument(
'--aln_mode',
type=str,
dest='aln_mode',
default='global',
choices=['local', 'global'],
help=
'Global/local read alignment (local, corresponds to the bowtie2 --local; global corresponds to the bowtie2 default --end-to-end).'
)
subparser.add_argument(
'--aln_interleaved',
action='store_true',
default=False,
help=
'FASTA/FASTQ file in -1 are paired and contain forward AND reverse reads'
)
# Pileup flags (samtools, or postprocessing)
subparser.add_argument(
'--aln_mapid',
dest='aln_mapid',
type=float,
metavar="FLOAT",
default=DEFAULT_ALN_MAPID,
help=
f"Discard reads with alignment identity < MAPID. Values between 0-100 accepted. ({DEFAULT_ALN_MAPID})"
)
subparser.add_argument(
'--aln_mapq',
dest='aln_mapq',
type=int,
metavar="INT",
default=DEFAULT_ALN_MAPQ,
help=f"Discard reads with mapping quality < MAPQ. ({DEFAULT_ALN_MAPQ})"
)
subparser.add_argument(
'--aln_readq',
dest='aln_readq',
type=int,
metavar="INT",
default=DEFAULT_ALN_READQ,
help=f"Discard reads with mean quality < READQ ({DEFAULT_ALN_READQ})")
subparser.add_argument(
'--aln_cov',
dest='aln_cov',
default=DEFAULT_ALN_COV,
type=float,
metavar="FLOAT",
help=
f"Discard reads with alignment coverage < ALN_COV ({DEFAULT_ALN_COV}). Values between 0-1 accepted."
)
subparser.add_argument(
'--aln_baseq',
dest='aln_baseq',
default=DEFAULT_ALN_BASEQ,
type=int,
metavar="INT",
help=f"Discard bases with quality < ALN_BASEQ ({DEFAULT_ALN_BASEQ})")
subparser.add_argument(
'--aln_trim',
dest='aln_trim',
default=DEFAULT_ALN_TRIM,
type=int,
metavar="INT",
help=
f"Trim ALN_TRIM base-pairs from 3'right end of read ({DEFAULT_ALN_TRIM})"
)
if False:
# This is unused.
subparser.add_argument('--aln_discard',
dest='aln_baq',
default=False,
help='Discard discordant read-pairs (False)')
subparser.add_argument(
'--aln_baq',
dest='aln_baq',
default=False,
help='Enable BAQ: per-base alignment quality (False)')
subparser.add_argument('--aln_adjust_mq',
dest='aln_adjust_mq',
default=False,
help='Adjust MAPQ (False)')
subparser.add_argument('--sparse',
dest='sparse',
default=False,
help=f"Omit zero rows from output.")
return main_func
def register_args(main_func):
subparser = add_subcommand('midas_run_genes', main_func, help='metagenomic pan-genome profiling')
subparser.add_argument('outdir',
type=str,
help="""Path to directory to store results. Name should correspond to unique sample identifier.""")
subparser.add_argument('-1',
dest='r1',
required=True,
help="FASTA/FASTQ file containing 1st mate if using paired-end reads. Otherwise FASTA/FASTQ containing unpaired reads.")
subparser.add_argument('-2',
dest='r2',
help="FASTA/FASTQ file containing 2nd mate if using paired-end reads.")
subparser.add_argument('--max_reads',
dest='max_reads',
type=int,
metavar="INT",
help=f"Number of reads to use from input file(s). (All)")
subparser.add_argument('--species_cov',
type=float,
dest='species_cov',
metavar='FLOAT',
default=DEFAULT_SPECIES_COVERAGE,
help=f"Include species with >X coverage ({DEFAULT_SPECIES_COVERAGE})")
if False:
# This is unused.
subparser.add_argument('--species_topn',
type=int,
dest='species_topn',
metavar='INT',
help='Include top N most abundant species')
# Alignment flags (bowtie, or postprocessing)
subparser.add_argument('--aln_cov',
dest='aln_cov',
default=DEFAULT_ALN_COV,
type=float,
metavar="FLOAT",
help=f"Discard reads with alignment coverage < ALN_COV ({DEFAULT_ALN_COV}). Values between 0-1 accepted.")
subparser.add_argument('--aln_readq',
dest='aln_readq',
type=int,
metavar="INT",
default=DEFAULT_ALN_READQ,
help=f"Discard reads with mean quality < READQ ({DEFAULT_ALN_READQ})")
subparser.add_argument('--aln_mapid',
dest='aln_mapid',
type=float,
metavar="FLOAT",
default=DEFAULT_ALN_MAPID,
help=f"Discard reads with alignment identity < MAPID. Values between 0-100 accepted. ({DEFAULT_ALN_MAPID})")
subparser.add_argument('--aln_mapq',
dest='aln_mapq',
type=int,
metavar="INT",
default=DEFAULT_ALN_MAPQ,
help=f"Discard reads with DEFAULT_ALN_MAPQ < MAPQ. ({DEFAULT_ALN_MAPQ})")
subparser.add_argument('--aln_speed',
type=str,
dest='aln_speed',
default='very-sensitive',
choices=['very-fast', 'fast', 'sensitive', 'very-sensitive'],
help='Alignment speed/sensitivity (very-sensitive). If aln_mode is local (default) this automatically issues the corresponding very-sensitive-local, etc flag to bowtie2.')
subparser.add_argument('--aln_mode',
type=str,
dest='aln_mode',
default='local',
choices=['local', 'global'],
help='Global/local read alignment (local, corresponds to the bowtie2 --local). Global corresponds to the bowtie2 default --end-to-end.')
subparser.add_argument('--aln_interleaved',
action='store_true',
default=False,
help='FASTA/FASTQ file in -1 are paired and contain forward AND reverse reads')
return main_func
def register_args(main_func):
add_subcommand(
'aws_batch_init',
main_func,
help="init AWS Batch instance (never run outside AWS Batch)")
return main_func
def register_args(main_func):
add_subcommand('collate_repgenome_markers',
main_func,
help='collate marker genes for repgresentative genomes')
return main_func