def build_parser(parser):
parser = add_database_args(parser)
input_group = parser.add_argument_group(
"Input options").add_mutually_exclusive_group()
input_group.add_argument(
'-t', '--tax-ids',
dest='taxids',
metavar='FILE-OR-LIST',
help="""File containing a whitespace-delimited list of
tax_ids (ie, separated by tabs, spaces, or newlines; lines
beginning with "#" are ignored). This option can also be
passed a comma-delited list of taxids on the command line.""")
input_group.add_argument(
'-i', '--seq-info', type=argparse.FileType('r'),
help="""Read tax_ids from sequence info file, minimally containing the
field "tax_id" """)
output_group = parser.add_argument_group(
"Output options").add_mutually_exclusive_group()
output_group.add_argument(
'-o', '--out',
type=argparse.FileType('w'),
default=sys.stdout,
metavar='FILE',
help="""headerless csv file containing old_id,new_id""")
def build_parser(parser):
parser = add_database_args(parser)
input_group = parser.add_argument_group('input options')
input_group.add_argument(
'-t', '--tax-ids', nargs='+',
help='one or more space-delimited tax_ids (eg "-t 47770 33945")')
input_group.add_argument(
'-f', '--tax-id-file', metavar='FILE', type=argparse.FileType('rt'),
help=('File containing a whitespace-delimited list of '
'tax_ids (ie, separated by tabs, spaces, or newlines.'))
input_group.add_argument(
'-i', '--seq-info',
type=argparse.FileType('rt'),
help=('Read tax_ids from sequence info file, minimally '
'containing a column named "tax_id"'))
output_group = parser.add_argument_group(
"Output options").add_mutually_exclusive_group()
output_group.add_argument(
'-o', '--outfile',
type=argparse.FileType('wt'),
default=sys.stdout,
metavar='FILE',
help=('Output file containing lineages for the specified taxa '
'in csv format; writes to stdout if unspecified'))
def build_parser(parser):
parser.add_argument(
'new_nodes',
metavar='csv',
help=('A csv file defining nodes to add to the taxonomy. '
'Mandatory fields include "tax_id", "parent_id", "rank", '
'"tax_name"; optional fields include "source_name", '
'"source_id" and "children". The "children" field should '
'specify one or more existing taxids in a semicolon-'
'delimited list. Other columns are ignored.'))
parser = add_database_args(parser)
parser.add_argument(
'-S', '--source-name',
dest='source_name',
default='unknown',
help=('Identifies the source for new nodes (will override '
'"source_name" in the input provided '
'by `--new-nodes`). [%(default)s]'))
parser.add_argument(
'--update',
action='store_true',
help='Update any existing nodes')
parser.add_argument(
'--tax-table',
help='table name in database')
parser.add_argument(
'--out',
default=sys.stdout,
help='sql queries')
def build_parser(parser):
parser = add_database_args(parser)
parser.add_argument('tax_ids', nargs='+')
parser.add_argument(
'-o', '--outfile',
type=argparse.FileType('w'),
default=sys.stdout,
metavar='FILE')
def build_parser(parser):
parser = add_database_args(parser)
node_parser = parser.add_argument_group(title='node options')
node_parser.add_argument('--valid',
action='store_true',
help='include only valid nodes')
node_parser.add_argument(
'--ranked',
action='store_true',
help='include only ranked nodes (drop no_rank nodes)')
input_group = parser.add_argument_group('input options')
input_group.add_argument('--taxtable',
metavar='CSV',
help='build from a previous built taxtable')
input_group.add_argument('--clade-ids',
help=('return top-down tax_id clades'))
input_group.add_argument(
'-n',
'--taxnames',
metavar='FILE',
help=('A file identifing taxa in the form of taxonomic '
'names. Names are matched against both primary names and '
'synonyms. Lines beginning with "#" are ignored. Taxa '
'identified here will be added to those specified using '
'--tax-ids'))
input_group.add_argument(
'-t',
'--tax-ids',
metavar='FILE-OR-LIST',
help=('File containing a whitespace-delimited list of '
'tax_ids (ie, separated by tabs, spaces, or newlines; lines '
'beginning with "#" are ignored). This option can also be '
'passed a comma-delited list of tax_ids on the command line.'))
input_group.add_argument(
'-i',
'--seq-info',
type=argparse.FileType('r'),
help=('Read tax_ids from sequence info file, minimally '
'containing the field "tax_id"'))
output_group = parser.add_argument_group(
"Output options").add_mutually_exclusive_group()
output_group.add_argument(
'-o',
'--out',
type=argparse.FileType('w'),
default=sys.stdout,
metavar='FILE',
help=('Output file containing lineages for the specified taxa '
'in csv format; writes to stdout if unspecified'))
def build_parser(parser):
parser = add_database_args(parser)
# TODO: do we need the commented-out options?
# node_parser = parser.add_argument_group(title='node options')
# node_parser.add_argument(
# '--valid',
# action='store_true',
# help='Include only valid nodes.')
# node_parser.add_argument(
# '--ranked',
# choices=['columns', 'rows'],
# help='Include only ranked columns or ranked rows and columns.')
input_group = parser.add_argument_group('input options')
# input_group.add_argument(
# '--taxtable',
# metavar='CSV',
# help='build from a previous built taxtable')
# input_group.add_argument(
# '--clade-ids',
# help=('return top-down tax_id clades'))
input_group.add_argument(
'-t',
'--tax-ids',
nargs='+',
help='one or more space-delimited tax_ids (eg "-t 47770 33945")')
input_group.add_argument(
'-f',
'--tax-id-file',
metavar='FILE',
type=argparse.FileType('rt'),
help=('File containing a whitespace-delimited list of '
'tax_ids (ie, separated by tabs, spaces, or newlines.'))
input_group.add_argument(
'-i',
'--seq-info',
type=argparse.FileType('rt'),
help=('Read tax_ids from sequence info file, minimally '
'containing a column named "tax_id"'))
output_group = parser.add_argument_group(
"Output options").add_mutually_exclusive_group()
output_group.add_argument(
'-o',
'--outfile',
type=argparse.FileType('wt'),
default=sys.stdout,
metavar='FILE',
help=('Output file containing lineages for the specified taxa '
'in csv format; writes to stdout if unspecified'))
def build_parser(parser):
parser = add_database_args(parser)
parser.add_argument(
'source_name',
help='name of source identifying names and nodes to extract')
parser.add_argument('-o',
'--outfile',
type=Opener('w'),
default=sys.stdout)
def build_parser(parser):
parser = add_database_args(parser)
parser.add_argument('new_nodes', metavar='FILE', type=Opener('r'),
help='yaml file specifying new nodes')
parser.add_argument(
'--source-name', dest='source_name',
help=("""Provides the default source name for new nodes. The
value is overridden by "source_name" in the input
file. If not provided, "source_name" is required in each
node or name definition. This source name is created if
it does not exist."""))
def build_parser(parser):
parser = add_database_args(parser)
parser.add_argument('new_nodes',
metavar='FILE',
type=Opener('r'),
help='yaml file specifying new nodes')
parser.add_argument(
'--source-name',
dest='source_name',
help=("""Provides the default source name for new nodes. The
value is overridden by "source_name" in the input
file. If not provided, "source_name" is required in each
node or name definition. This source name is created if
it does not exist."""))
def build_parser(parser):
parser = add_database_args(parser)
parser.add_argument('source_name',
help='name of source identifying names and nodes to extract')
parser.add_argument('-o', '--outfile', type=Opener('w'), default=sys.stdout)