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('source_name', help='name of source identifying names and nodes to extract') parser.add_argument('-o', '--outfile', type=Opener('w'), default=sys.stdout)