rotifer.db.cli.rneighbors

class rotifer.db.cli.rneighbors

Bases: object

Argument parser builder for the rneighbors program.

The options cover the input file of protein accessions, the size of the neighborhood (--above and --below), filters by genomic accession or assembly, output format selection and logging destinations.

input(number=1, exclude=[], input_order=['file', 'above', 'below', 'gacc', 'asm', 'debug', 'outformat', 'log'], add_help=False, no_open=False)

Build an argument parser with the rneighbors options.

Parameters:

numberint, default 1

Unused, kept for interface compatibility.

excludelist of str, default []

Option names to leave out of the parser.

input_orderlist of str, optional

Options to add, in order. Defaults to every available option: file, above, below, gacc, asm, debug, outformat and log.

add_helpbool, default False

Whether the parser defines its own --help option.

no_openbool, default False

When True, the --genomic_accession and --assembly options take plain values instead of files loaded through rotifer.core.cli.

Returns:

argparse.ArgumentParser

The configured parser.