mode_info.txt

SYNOPSIS

    metacache info [<database> ]
    metacache info [<database> reference [<sequence_id>]... ]
    metacache info [<database> rank <rank_name> ]
    metacache info [<database> lineages ]
    metacache info [<database> statistics ]
    metacache info [<database> locations ]
    metacache info [<database> featurecounts ]


DESCRIPTION

    Display (meta-)information stored in a database.


SUB-MODES

    metacache info
        show basic properties of MetaCache executable (data type widths, etc.)

    matacache info <database>
        show basic properties of <database>

    matacache info <database> ref[erence]
       list meta information for all reference sequences in <database>

    matacache info <database> ref[erence] <sequence_id>...
       list meta information for specific reference sequences

    matacache info <database> rank <rank_name>
       list reference sequence distribution on rank <rank_name>

    matacache info <database> lin[eages]
       print table with ranked lineages for all reference sequences

    matacache info <database> stat[istics]
       print database statistics / hash table properties

    matacache info <database> loc[ations]
       print map (feature -> list of reference locations)
       Not available in the GPU version.

    matacache info <database> featurecounts
       print map (feature -> number of reference locations)
       Not available in the GPU version.


PARAMETERS

    <database>        database file name;
                      A MetaCache database contains taxonomic information and
                      min-hash signatures of reference sequences (complete
                      genomes, scaffolds, contigs, ...).

    <rank_name>       Valid values: sequence, form, variety, subspecies,
                      species, subgenus, genus, subtribe, tribe, subfamily,
                      family, suborder, order, subclass, class, subphylum,
                      phylum, subkingdom, kingdom, domain


EXAMPLES

    List metadata for all reference sequences in database 'refseq':
        metacache info refseq ref

    List metadata for the sequence with id NC_12345.6 in database 'refseq':
        metacache info refseq ref NC_12345.6

    List distribution of the number of sequences on rank 'phylum':
        metacache info refseq rank phylum