metagenome.py

"""summarize metagenome gather results"""

usage = """

    sourmash tax metagenome --gather-csv <gather_csv> [ ... ] --taxonomy-csv <taxonomy-csv> [ ... ]

The 'tax metagenome' command reads in metagenome gather result CSVs and
summarizes by taxonomic lineage.

The default output format consists of four columns,
 'query_name,rank,fraction,lineage', where 'fraction' is the fraction
 of the query matched to that reported rank and lineage. The summarization
 is reported for each taxonomic rank.

Alternatively, you can output results at a specific rank (e.g. species)
in 'krona', 'lineage_summary', and 'human' formats.

Use '-F human' to display human-readable output.

Please see the 'tax metagenome' documentation for more details:
  https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-tax-metagenome-summarize-metagenome-content-from-gather-results
"""

import sourmash
from sourmash.logging import notify, print_results, error
from sourmash.cli.utils import add_rank_arg, check_rank, check_tax_outputs


def subparser(subparsers):
    subparser = subparsers.add_parser("metagenome", usage=usage)
    subparser.add_argument(
        "-g",
        "--gather-csv",
        action="extend",
        nargs="*",
        default=[],
        help="CSVs from sourmash gather",
    )
    subparser.add_argument(
        "--from-file",
        metavar="FILE",
        default=None,
        help="input many gather results as a text file, with one gather CSV per line",
    )
    subparser.add_argument(
        "-q", "--quiet", action="store_true", help="suppress non-error output"
    )
    subparser.add_argument(
        "-o",
        "--output-base",
        default="-",
        help="base filepath for output file(s) (default stdout)",
    )
    subparser.add_argument(
        "--output-dir", default="", help="directory for output files"
    )
    subparser.add_argument(
        "-t",
        "--taxonomy-csv",
        "--taxonomy",
        metavar="FILE",
        action="extend",
        nargs="+",
        required=True,
        help="database lineages CSV",
    )
    subparser.add_argument(
        "--keep-full-identifiers",
        action="store_true",
        help="do not split identifiers on whitespace",
    )
    subparser.add_argument(
        "--keep-identifier-versions",
        action="store_true",
        help="after splitting identifiers, do not remove accession versions",
    )
    subparser.add_argument(
        "--fail-on-missing-taxonomy",
        action="store_true",
        help="fail quickly if taxonomy is not available for an identifier",
    )
    subparser.add_argument(
        "-F",
        "--output-format",
        default=[],
        nargs="*",
        action="extend",
        choices=[
            "human",
            "csv_summary",
            "krona",
            "lineage_summary",
            "kreport",
            "lingroup",
            "bioboxes",
        ],
        help="choose output format(s)",
    )
    subparser.add_argument(
        "-f",
        "--force",
        action="store_true",
        help="continue past errors in taxonomy database loading",
    )
    subparser.add_argument(
        "--lins",
        "--lin-taxonomy",
        action="store_true",
        default=False,
        help="use LIN taxonomy in place of standard taxonomic ranks.  Note that the taxonomy CSV must contain 'lin' lineage information.",
    )
    subparser.add_argument(
        "--lingroup",
        "--lingroups",
        metavar="FILE",
        default=None,
        help="CSV containing 'name', 'lin' columns, where 'lin' is the lingroup prefix. Will produce a 'lingroup' report containing taxonomic summarization for each group.",
    )
    subparser.add_argument(
        "--ictv",
        "--ictv-taxonomy",
        action="store_true",
        default=False,
        help="use ICTV taxonomy in place of standard taxonomic ranks.  Note that the taxonomy CSV must contain ICTV ranks.",
    )
    add_rank_arg(subparser)


def main(args):
    try:
        if not args.gather_csv and not args.from_file:
            raise ValueError(
                "No gather CSVs found! Please input via '-g' or '--from-file'."
            )
        if args.rank:
            args.rank = check_rank(args)
        args.output_format = check_tax_outputs(
            args,
            rank_required=["krona", "lineage_summary"],
            incompatible_with_lins=["bioboxes", "kreport"],
            use_lingroup_format=True,
        )

    except ValueError as exc:
        error(f"ERROR: {str(exc)}")
        import sys

        sys.exit(-1)

    return sourmash.tax.__main__.metagenome(args)