taxify

Usage

usage: blobtools taxify          -f FILE [-a INT] [-b INT] [-c INT]
                                    [-m FILE] [-s INT] [-t INT]
                                    [-i FILE] [-x INT] [-v FLOAT]
                                    [-o PREFIX] [-h|--help]

    Options:
        -h --help                           show this

    Options for similarity search input
        -f, --hit_file <FILE>               BLAST/Diamond similarity search result (TSV format).
                                                Defaults assume "-outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore'"
        -a, --hit_column_qseqid <INT>       Zero-based column of qseqid in similarity search result [default: 0]
                                                Change if different format than (-outfmt '6')
        -b, --hit_column_sseqid <INT>       Zero-based column of sseqid in similarity search result [default: 1]
                                                Change if different format than (-outfmt '6')
        -c, --hit_column_score <INT>        Zero-based column of (bit)score in similarity search result [default: 11]
                                                Change if different format than (-outfmt '6')
    Options for TaxID mapping file
        -m, --taxid_mapping_file <FILE>     TaxID mapping file (contains seqid and taxid)
        -s, --map_col_sseqid <INT>          Zero-based column of sseqid in TaxID mapping file (it will search for sseqid in this column)
        -t, --map_col_taxid <INT>           Zero-based Column of taxid in TaxID mapping file (it will extract for taxid from this column)

    Options for custom input
        -i, --custom <FILE>                 File containing list of sequence IDs
        -x, --custom_taxid <INT>            TaxID to assign to all sequence IDs in list
        -v, --custom_score <FLOAT>          Score to assign to all sequence IDs in list

    General
        -o, --out <PREFIX>                  Output prefix

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Comments

See TaxID-mapping file for an example

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