def build_parser(parser):
parser.add_argument('fastq',
nargs='?',
default=sys.stdin,
type=Opener('r'),
help='fastq-sanger file with phred scores')
parser.add_argument('-o',
'--out',
default=sys.stdout,
type=Opener('w'),
help='csv-format file containing stats for each read.')
parser.add_argument('-l',
'--limit',
type=int,
metavar='N',
help='Limit number of sequences read from input to N')
parser.add_argument(
'-e',
'--extra-fields',
type=str,
help="extra fields for csv file in form 'name1:val1,name2:val2'")
parser.add_argument('-n',
'--no-header',
action='store_false',
default=True,
dest='show_header')
def build_parser(parser):
parser.add_argument('raw_reads',
type=lambda f: fastalite(Opener()(f)),
help="""input fasta file containing original
clustered reads (default stdin).""")
parser.add_argument('readmap',
type=Opener('r'),
help="""output of `bioy denoise --readmap`
(csv file with columns readname,clustername)""")
parser.add_argument('-r',
'--rlefile',
type=Csv2Dict('name',
'rle',
fieldnames=['name', 'rle']),
help="""An optional file containing run
length encoding for infile (.csv.bz2)""")
parser.add_argument('-d', '--outdir', help='output directory', default='.')
parser.add_argument('--pattern',
help="""A regular expression matching cluster names""")
parser.add_argument('-N',
'--sample',
type=int,
default=100,
metavar='N',
help='inculde no more than N reads [%(default)s]')
parser.add_argument('--name-suffix',
help='string to insert into name before .fasta',
default='aln')
parser.add_argument('--no-align',
action='store_false',
dest='align',
default=True)
def build_parser(parser):
parser.add_argument('tree',
default=sys.stdin,
nargs='?',
type=Opener('r'),
help='sequences in fasta format')
parser.add_argument('--info',
type=Opener('r'),
metavar='CSV',
help="""selectively replace leaves from a two column
csv [seqname,*newname*] *optional column*""")
parser.add_argument('-o',
'--out',
default='/dev/stdout',
help='output file [%(default)s]')
parser.add_argument('--add-prefix',
default='',
metavar='PRE',
help='append a prefix string to all names')
parser.add_argument('--add-suffix',
default='',
metavar='SUF',
help='append a suffix string to all names')
parser.add_argument('--tree-type',
default='newick',
help='tree type to parse')
parser.add_argument('--remove-word',
metavar='REGEX',
help='remove a word from a ')
def build_parser(parser):
parser.add_argument('fasta',
type=lambda f: fastalite(Opener()(f)),
help='input fasta file')
parser.add_argument('-l',
'--left-aligns',
type=Opener(),
help='left primer ssearch36 alignment results')
parser.add_argument('-r',
'--right-aligns',
type=Opener(),
help='right primer ssearch36 alignment results')
parser.add_argument('--left-range',
metavar='START,STOP',
help='Range of acceptable left primer start positions')
parser.add_argument('--left-zscore',
metavar='VALUE',
type=float,
help='Min acceptable left primer z-score')
parser.add_argument('--right-range',
metavar='START,STOP',
help=('Range of acceptable right '
'primer start positions'))
parser.add_argument('--right-zscore',
metavar='VALUE',
type=float,
help='Min acceptable right primer z-score')
parser.add_argument('--left-expr',
help=('python expression defining '
'criteria for keeping left primer'))
parser.add_argument('--right-expr',
help=('python expression defining criteria '
'for keeping left primer'))
parser.add_argument('-o',
'--fasta-out',
type=Opener('w'),
default=sys.stdout,
help='trimmed fasta output file')
parser.add_argument('--rle',
type=Csv2Dict('name',
'rle',
fieldnames=['name', 'rle']),
help='rle input file (required if --rle-out)')
parser.add_argument(
'--rle-out',
type=lambda f: DictWriter(Opener('w')(f), fieldnames=['name', 'rle']),
help='trimmed rle output file')
parser.add_argument('-i',
'--include-primer',
action='store_true',
default=False,
help='Include primer in trimmed sequence')
parser.add_argument('--keep-all-seqs',
action='store_true',
help='keep seqs that outside the trimming thresholds')
def build_parser(parser):
parser.add_argument('alignments',
default=sys.stdin,
type=Opener('r'),
nargs='?',
help='ssearch -m 10 formatted file')
parser.add_argument('-o',
'--out',
default=sys.stdout,
type=Opener('w'),
help='(default csv)-formatted output')
parser.add_argument('-p',
'--print-one',
default=False,
action='store_true',
help='pretty print first alignment and exit')
parser.add_argument(
'-f',
'--fieldnames',
type=lambda f: f.split(','),
help='comma-delimited list of field names to include in output')
parser.add_argument('--limit',
type=int,
metavar='N',
help='Print no more than N alignments')
parser.add_argument('--no-header', dest='header', action='store_false')
parser.add_argument('-r',
'--rlefile',
type=Csv2Dict(index='name',
value='rle',
fieldnames=['name', 'rle']),
nargs='+',
help='CSV file containing run-length encoding')
parser.add_argument('--min-zscore',
default=None,
type=float,
metavar='X',
help='Exclude alignments with z-score < X')
parser.add_argument('-a',
'--top-alignment',
default=False,
action='store_true',
help="""By default, return all alignments;
provide this option to include
only the top entry per query.""")
parser.add_argument(
'-e',
'--extra-fields',
help="extra fields for csv file in form 'name1:val1,name2:val2'")
parser.add_argument('-d',
'--with-diff',
action='store_true',
default=False,
help="""add fields 'q_diff' and 't_diff' containing
aligned substrings with mismatches in lowercase""")
def build_parser(parser):
parser.add_argument('infile',
type=Opener('r'),
default=sys.stdin,
nargs='?',
help='File containing stdout of call to cmalign')
parser.add_argument('-o',
'--outfile',
type=Opener('w'),
default=sys.stdout,
help='Output file in csv format (default is stdout)')
def build_parser(parser):
parser.add_argument('csv',
default = sys.stdin,
nargs = '?',
type = Opener(),
help = 'input tsv file')
parser.add_argument('-o', '--out',
type = Opener('w'),
default = sys.stdout,
help = 'csv file')
parser.add_argument('--split-column',
help = 'column:delimiter:*newcolumns')
def build_parser(parser):
parser.add_argument('seqs',
type=lambda f: fastalite(Opener()(f), readfile=False),
help='Input fasta file')
parser.add_argument(
'rle',
type=Opener(),
help='csv file (may be bzip encoded) containing columns "name","rle"')
parser.add_argument('-o',
'--outfile',
type=Opener('w'),
default=sys.stdout,
help='Name of output file')
def build_parser(parser):
parser.add_argument('query', help='input fasta query file')
parser.add_argument('library',
help='input fasta library file to search against')
parser.add_argument('-o',
'--out',
type=Opener('w'),
default=sys.stdout,
help='tabulated ssearch results')
parser.add_argument('--no-header',
dest='header',
action='store_false',
default=True,
help='no header')
parser.add_argument(
'--all-alignments',
action='store_true',
help='maximum number of alignments to keep default = 1')
parser.add_argument('-g',
'--gap-extension-penalty',
default='4',
help='gap extension penalty default = %(default)s')
parser.add_argument('-f',
'--gap-open-penalty',
default='12',
help='gap open penalty default = %(default)s')
parser.add_argument('-a',
'--full-sequences',
default=False,
action='store_true',
help='return full sequences in alignment')
parser.add_argument('-O',
'--out-raw',
type=Opener('w'),
help='return raw ssearch output')
parser.add_argument('--decode',
type=Csv2Dict(index='name',
value='rle',
fieldnames=['name', 'rle']),
help='Decode alignment')
parser.add_argument(
'--fieldnames',
type=lambda f: f.split(','),
help='comma-delimited list of field names to include in output')
parser.add_argument('--min-zscore',
default=0,
type=float,
metavar='X',
help='Exclude alignments with z-score < X')
def build_parser(parser):
parser.add_argument('csv',
nargs='?',
default=sys.stdin,
metavar='FILE',
type=Opener(),
help='A csv file with at least one column')
parser.add_argument('--columns',
default='1,2',
help='Comma-delimited list of column names or numbers')
parser.add_argument('--out',
metavar='FILE',
type=Opener('w'),
default=sys.stdout,
help='output fasta file')
def build_parser(parser):
parser.add_argument('fasta',
metavar='FILE',
type=Opener(),
help='input fasta')
parser.add_argument('specimen_map',
metavar='CSV',
type=Opener(),
help='columns: readname, specimen')
parser.add_argument(
'--outdir',
metavar='DIR',
help=
'output folder for specimen fasta files, name being specimen.fasta.bz2',
default='.')
def build_parser(parser):
parser.add_argument('fasta',
nargs = '?',
default = sys.stdin,
metavar = 'FILE',
type = Opener(),
help = 'A fasta file')
parser.add_argument('--get',
action = 'append',
help = 'columname[:newname]')
parser.add_argument('--out',
metavar = 'FILE',
type = Opener('w'),
default = sys.stdout,
help = 'output csv file columns: [id,description,seq]')
def build_parser(parser):
parser.add_argument('sseqids', nargs='?', type=Opener('r'),
default = sys.stdin,
help = 'csv input file, each line containing gb,seq_start,seq_stop')
parser.add_argument('-o', '--outfasta',
type = Opener('w'),
default = sys.stdout,
help = 'multi-fasta, one sequence for each provided identifier')
parser.add_argument('-i', '--seqinfo',
type = Opener('w'),
help = "optionally output seqinfo for each sequence : {}".format(FETCH_HEADERS))
parser.add_argument('-n', '--no-header',
help = "suppress seqinfo header")
parser.add_argument('-e', '--email', required=True,
help = "users of NCBI Entrez API should provide email. if usage is excessive, ncbi may block access to its API")
def build_parser(parser):
parser.add_argument('infile',
default=sys.stdin,
nargs='?',
type=Opener(),
help='input csv file')
parser.add_argument(
'-o',
'--outfile',
help='HDF5 file [use basename of input file by default]')
parser.add_argument('-d',
'--outdir',
help="""Optional output directory. Ignored
if -o/--outfile is specified.""")
parser.add_argument('--fieldnames',
help='comma-delimited list of field names.')
parser.add_argument('-H',
'--no-header',
action='store_true',
default=False,
help="""indicate that the input file has no
header row. Uses value of --fieldnames if provided.""")
parser.add_argument('-k',
'--key',
default='data',
help="""A label identifing this table in the
data store "[%(default)s]" """)
parser.add_argument('-c',
'--no-compress',
action='store_false',
default=True,
dest='compress',
help="""Don't compress data store.""")
def build_parser(parser):
parser.add_argument(
'taxids',
type=lambda l: set(l.split(',')),
help='comma delimited list of column names to group columns')
parser.add_argument('taxonomy',
metavar='CSV',
default=sys.stdin,
nargs='?',
type=Opener(),
help='input classify csv file')
parser.add_argument('-o',
'--out',
type=Opener('w'),
default=sys.stdout,
help="""csv with columns
[parent_name,parent_id,parent_rank,tax_name,tax_id,rank]""")
def build_parser(parser):
parser.add_argument('infiles',
nargs='*',
default=[sys.stdin],
type=Opener(),
help='Input fasta file')
parser.add_argument('-o',
'--outfile',
type=Opener('w'),
default=sys.stdout,
help='Name of output file; default: %(default)s')
parser.add_argument(
'-r',
'--rlefile',
type=lambda f: DictWriter(Opener('w')(f), fieldnames=['name', 'rle']),
help="""Name of output file for run length encoding; default is to
append .csv.bz2 to --outfile basename.""")
def build_parser(parser):
parser.add_argument('fasta', default = sys.stdin, type = Opener('r'),
nargs = '?', help='sequences in fasta format')
parser.add_argument('-o', '--out', default = sys.stdout, type = Opener('w'),
help='output file (default stdout)')
parser.add_argument('--matrix-out', type = Opener('w'),
help = """median score of pairwise alignments""")
parser.add_argument('--primary-group', metavar = 'COLUMN_NAME',
help = """column in split_info to use for grouping""")
parser.add_argument('--secondary-group', metavar = 'COLUN_NAME',
help = """column in split_info to use for grouping if
primary_group is undefined for a given row""")
parser.add_argument('--split-info', metavar = 'FILE', type = Opener(),
help = """csv file containing column "seqname" plus another
column for grouping sequences prior to deduplication """)
parser.add_argument('-d', '--distance', action = 'store_true', default = False,
help = 'Calculate distance rather than identity.')
def build_parser(parser):
parser.add_argument(
'clusters', type=Opener(),
help='Clusters file (output of "usearch -uc")')
parser.add_argument(
'--fasta-in', type=lambda f: fastalite(Opener()(f)),
help='input fasta file containing original clustered reads')
parser.add_argument(
'--fasta-out', type=Opener('w'),
help='Output fasta containing centroids')
parser.add_argument(
'-g', '--groups', metavar='FILE', type=Opener(),
help="""An optional file defining groups for partitioning
input reads. If provided, cluster weights will be normalized
to proportionally represent each group. File is a headerless
csv with columns "seqname","group" (.csv.bz2)""")
parser.add_argument(
'--min-clust-size', type=int,
default=1, help='[%(default)s]')
parser.add_argument(
'-o', '--out', type=Opener('w'), default=sys.stdout,
help='Output file with columns (readname,centroidname)')
parser.add_argument(
'--specimenmap', type=Opener('w'),
help='Output file with columns (clustername,samplename)')
parser.add_argument(
'--specimen', metavar='SAMPLENAME',
help='provides samplename for mapfile')
parser.add_argument(
'-w', '--weights', type=Opener('w'),
help='Output file with columns (clustername,weight)')
def build_parser(parser):
parser.add_argument('csv',
default = sys.stdin,
nargs = '?',
type = Opener(),
help = 'input tsv file')
parser.add_argument('-o', '--out',
type = Opener('w'),
default = '/dev/stdout',
help = 'csv file')
parser.add_argument('--value',
help = 'value to pivot on for each row and column')
parser.add_argument('--rows',
help = 'comma delimited list of values')
parser.add_argument('--cols',
help = 'comma delimited list of values')
parser.add_argument('--fill-value',
help = 'if no pivot value')
def build_parser(parser):
parser.add_argument('seqs',
help='Input fasta file')
parser.add_argument('--is-file', action='store_true',
help=('if input is a fasta file. '
'Note: Output will also be fasta'))
parser.add_argument('--rlefile', type=Opener(),
help=('csv file (may be bzip encoded) '
'containing columns "name","rle"'))
parser.add_argument('-O', '--out-rle',
type=Opener('w'), help='reversed rlefile')
parser.add_argument('-o', '--out-fasta',
type=Opener('w'),
default=sys.stdout,
help='Name of fasta output file')
parser.add_argument('--out',
type=Opener('w'),
default=sys.stdout,
help='Name of output file')
def build_parser(parser):
parser.add_argument(
'infile',
type=Opener(),
nargs='?',
default=sys.stdin,
help=('csv file with ssearch36 columns '
'[q_name,q_seq,t_name,t_seq,q_al_start,q_al_stop,'
't_al_start,t_al_stop,t_sq_len,sw_zscore]'))
parser.add_argument(
'-i', '--info',
type=Opener(),
metavar='CSV',
help='info file mapping seqname to tax_id')
parser.add_argument(
'-t', '--taxonomy',
metavar='CSV',
type=Opener(),
help='taxonomy file mapping tax_id to taxonomy')
parser.add_argument(
'-o', '--out',
metavar='CSV',
type=Opener('w'),
default=sys.stdout,
help='csv output of bases {tax_id, species, positions,,}')
parser.add_argument(
'-r', '--rank',
default='species',
help='Aggregate primer stats by specified rank. [%(default)s]')
parser.add_argument(
'-f', '--position-freq',
metavar='FLOAT',
default=0.05,
type=float,
help='Minimum base frequency reported for a position [%(default)s]')
parser.add_argument(
'-z', '--min-zscore',
type=float,
help='Minimum z-score value to include alignment in base count.',
default=0)
def build_parser(parser):
parser.add_argument('query',
help='input fasta query file')
parser.add_argument('library',
help='input fasta library file to search against')
parser.add_argument('-o', '--out',
type=Opener('w'),
default=sys.stdout,
help='tabulated ssearch results')
parser.add_argument('--no-header',
dest='header',
action='store_false',
default=True,
help='no header')
parser.add_argument('--all-alignments',
action='store_true',
help='maximum number of alignments to keep [1]')
parser.add_argument('-g', '--gap-extension-penalty',
default='4',
help='gap extension penalty [%(default)s]')
parser.add_argument('-f', '--gap-open-penalty',
default='12',
help='gap open penalty [%(default)s]')
parser.add_argument('-a', '--full-sequences',
default=False,
action='store_true',
help='return full sequences in alignment')
parser.add_argument('--decode',
type=Csv2Dict(index='name', value='rle',
fieldnames=['name', 'rle']),
help='Decode alignment')
parser.add_argument('--fieldnames',
default=('q_name,t_name,sw_zscore,sw_overlap,'
'q_al_start,q_al_stop,sw_ident,qcovs,sw_frame'),
type=lambda f: f.split(','),
help=('comma-delimited list of field '
'names to include in output'))
parser.add_argument('-z', '--statistical-calculation',
default='1',
help="""built in statistical calculation
of E values for sequences. [%(default)s]""")
parser.add_argument('--min-zscore',
default=0,
type=float,
metavar='X',
help=('Exclude alignments with '
'z-score < X [%(default)s]'))
parser.add_argument('--strand',
default='forward',
choices=['forward','both'])
def build_parser(parser):
# required inputs
parser.add_argument(
'taxonomy',
help='must have tax_id column and rank columns')
parser.add_argument(
'thresholds',
help='with required columns tax_id, low, target_rank')
# common outputs
parser.add_argument(
'-o', '--out',
default=sys.stdout, type=Opener('w'), metavar='FILE',
help="Classification results.")
def build_parser(parser):
parser.add_argument('fasta', default='-', help='input fasta file')
parser.add_argument(
'-o',
'--out',
type=Opener('w'),
default=sys.stdout,
help='tabulated BLAST results with the following default headers {}'.
format(BLAST_HEADER_DEFAULT))
parser.add_argument('-d',
'--database',
help='blast database path for local blasts')
parser.add_argument(
'-r',
'--remote-database',
choices=['nt', 'nr'],
help='type of remote database to use, if remote flag provided')
parser.add_argument(
'--limit',
type=int,
help='maximum number of query sequences to read from the alignment')
parser.add_argument('--header', action='store_true', help='output header')
parser.add_argument(
'--strand',
default='plus',
choices=['plus', 'minus', 'both'],
help="""query strand(s) to search against database/subject.
default = %(default)s""")
parser.add_argument(
'--id',
default='90',
help='minimum identity for accepted values [%(default)s]')
parser.add_argument(
'--max', help='maximum number of alignments to keep default = (all)')
parser.add_argument('-n',
'--dry-run',
action='store_true',
help='print blast command and exit')
parser.add_argument('--nohits', action='store_true', help='')
parser.add_argument(
'--coverage',
type=float,
help='minimum coverage for accepted values [%(default)s]')
parser.add_argument('--outfmt',
default=BLAST_FORMAT_DEFAULT,
help='A comma delimited list of field names to output')
parser.add_argument('--remote',
action='store_true',
help='execute query on remote NCBI server')
def build_parser(parser):
parser.add_argument('infile',
type=Opener(),
nargs='?',
default=sys.stdin,
help='input fasta file (default %(default)s).')
parser.add_argument('outfile',
type=Opener('w'),
default=sys.stdout,
nargs='?',
help='Output fasta file.')
parser.add_argument('-r',
'--rlefile',
type=Opener(),
help=('An optional file containing run length '
'encoding for infile (.json.bz2)'))
parser.add_argument('-n',
'--seqname',
help=('Name for the output sequence. '
'Default basename(infile).replace(".fasta","") '
'if infile is provided, otherwise "consensus"'))
parser.add_argument('--gaps',
action='store_true',
help='retain gaps in consensus sequence')
def build_parser(parser):
parser.add_argument('fasta',
type=lambda f: fastalite(opener(f)),
help='input file containing raw reads')
parser.add_argument('--sample-id', help='sample id to pull reads for')
parser.add_argument(
'--map-file',
type=Csv2Dict(value='sample_id',
fieldnames=['sequence_id', 'sample_id']),
help='csv(.bz2) file containing sequence_id,sample_id in the rows.')
parser.add_argument('-o',
'--out',
type=Opener('w'),
default=sys.stdout,
help='fasta output file')
def build_parser(parser):
parser.add_argument('aligns',
nargs='?',
default=sys.stdin,
type=Opener('r'),
help='csvfile of ssearch results')
parser.add_argument(
'-o',
'--out',
default=sys.stdout,
type=Opener('w'),
help='csv file tallying each error category for each read')
parser.add_argument(
'-m',
'--homopolymer-matrix',
dest='matrix',
type=lambda f: writer(Opener('w')(f)),
help='csv file containing transition matrix of homopolymer lengths')
parser.add_argument(
'-M',
'--homopolymer-max',
default=6,
type=int,
help='csv homopolymer length above which counts are binned')
parser.add_argument('--step',
action='store_true',
help='step through reults (for debugging)')
parser.add_argument(
'-f',
'--extra-fields',
type=lambda f: parse_extras(f),
default={},
help="extra fields for csv file in form 'name1:val1,name2:val2'")
parser.add_argument('--output-alignment',
action='store_true',
help='Include the actual alignment in csv output')
def build_parser(parser):
parser.add_argument('infile',
default=sys.stdin,
type=Opener(),
nargs='?',
help='input csv file')
parser.add_argument(
'-o', '--outfile', default='-', help='output csv file',)
parser.add_argument('-a', '--add', metavar='FIELD_SPEC',
help=("new fields for csv file in form "
"'name1:val1,name2:val2,...'"))
parser.add_argument('-r', '--rename', metavar='FIELD_SPEC',
help=("fields to rename in the format "
"'from1:to1,from2:to2,...'"))
parser.add_argument('-i', '--inplace', action='store_true', default=False,
help='modify input file in place [%(default)s]')
def build_parser(parser):
parser.add_argument('sequences',
type=Opener(),
default=sys.stdin,
help='input fasta file')
parser.add_argument('-i',
'--split-info',
metavar='FILE',
type=Opener('rU'),
help="""csv file containing column "seqname" plus
another column for grouping sequences prior to deduplication"""
)
parser.add_argument(
'--primary-group',
metavar='COLUMN_NAME',
help='column in split_info to use for grouping [default %(default)s]',
default='species')
parser.add_argument('--secondary-group',
metavar='COLUMN_NAME',
help="""column in split_info to use for grouping
if primary_group is undefined
for a given row [default %(default)s]""",
default='tax_id')
parser.add_argument(
'--out-map',
metavar='FILE',
type=Opener('w'),
help='map file of sequences from (kept_seq_id,orig_seq_i)')
parser.add_argument('--out-weights',
metavar='FILE',
help='weight file for each kept sequence',
type=Opener('w'))
parser.add_argument('-O',
'--out-info',
metavar='FILE',
type=Opener('w'),
help='deduplicate seq info file')
parser.add_argument('-o',
'--out',
metavar='FILE',
type=Opener('w'),
default=sys.stdout,
help='deduplicated sequences in fasta format')
def build_parser(parser):
parser.add_argument(
'blast_file',
nargs='?',
default=sys.stdin,
type=Opener('r'),
help='CSV tabular blast file of query and subject hits')
parser.add_argument(
'--all-one-group',
dest='all_one_group',
action='store_true',
help="""If --map is not provided, the default behavior is to treat
all reads as one group; use this option to treat
each read as a separate group [%(default)s]""")
parser.add_argument(
'-a',
'--asterisk',
default=100,
metavar='PERCENT',
type=float,
help='Next to any species above a certain threshold [%(default)s]')
parser.add_argument('--copy-numbers',
metavar='CSV',
type=Opener(),
help='columns: tax_id, median')
parser.add_argument(
'-c',
'--coverage',
default=95,
metavar='PERCENT',
type=float,
help='percent of alignment coverage of blast result [%(default)s]')
parser.add_argument(
'--details-identity',
metavar='PERCENT',
help='Minimum identity to include blast hits in details file',
type=float,
default=90)
parser.add_argument(
'--details-full',
action='store_true',
help='do not limit out_details to only larget cluster per assignment')
parser.add_argument('--exclude-by-taxid',
metavar='CSV',
type=lambda f: set(e for e in DictReader(
opener(f), fieldnames='tax_id')),
default={},
help='column: tax_id')
parser.add_argument(
'--group-def',
metavar='INT',
action='append',
default=[],
help="""define a group threshold for a particular rank overriding
--target-max-group-size. example: genus:2""")
parser.add_argument('--group-label',
metavar='LABEL',
default='all',
help='Single group label for reads')
parser.add_argument(
'-o',
'--out',
default=sys.stdout,
type=Opener('w'),
metavar='CSV',
help="""columns: specimen, max_percent, min_percent, max_coverage,
min_coverage, assignment_id, assignment, clusters, reads,
pct_reads, corrected, pct_corrected, target_rank, hi, low, tax_ids"""
)
parser.add_argument('-m',
'--map',
metavar='CSV',
type=Opener(),
default={},
help='columns: name, specimen')
parser.add_argument(
'--max-ambiguous',
metavar='INT',
default=3,
type=int,
help='Maximum ambiguous count in reference sequences [%(default)s]')
parser.add_argument(
'--max-identity',
default=100,
metavar='PERCENT',
type=float,
help='maximum identity threshold for accepting matches [<= %(default)s]'
)
parser.add_argument(
'--min-cluster-size',
default=0,
metavar='INT',
type=int,
help='minimum cluster size to include in classification output')
parser.add_argument(
'--min-identity',
default=99,
metavar='PERCENT',
type=float,
help='minimum identity threshold for accepting matches [> %(default)s]'
)
parser.add_argument(
'-s',
'--seq-info',
required=True,
metavar='CSV',
type=Opener(),
help='seq info file(s) to match sequence ids to taxids [%(default)s]')
parser.add_argument(
'-t',
'--taxonomy',
required=True,
metavar='CSV',
type=Csv2Dict('tax_id'),
help='tax table of taxids and species names [%(default)s]')
parser.add_argument(
'-O',
'--out-detail',
type=lambda f: DictWriter(
opener(f, 'w'),
extrasaction='ignore',
fieldnames=[
'specimen', 'assignment', 'assignment_id', 'qseqid', 'sseqid',
'pident', 'coverage', 'ambig_count', 'accession', 'tax_id',
'tax_name', 'target_rank', 'rank', 'hi', 'low'
]),
metavar='CSV',
help="""columns: specimen, assignment, assignment_id,
qseqid, sseqid, pident, coverage, ambig_count,
accession, tax_id, tax_name, target_rank, rank, hi, low"""
)
parser.add_argument('--target-max-group-size',
metavar='INTEGER',
default=3,
type=int,
help="""group multiple target-rank assignments that
excede a threshold to a higher rank [%(default)s]""")
parser.add_argument(
'--target-rank',
metavar='RANK',
help='Rank at which to classify. Default: "%(default)s"',
default='species')
parser.add_argument('-w',
'--weights',
metavar='CSV',
type=Opener(),
help='columns: name, weight')
### csv.Sniffer.has_header is *not* reliable enough
parser.add_argument('--has-header',
action='store_true',
help='specify this if blast data has a header')