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bin/physeter.pl  view on Meta::CPAN

        }

        # skip extra (unused) relatives
        if (@relatives >= $ARGV_tax_max_hits) {
            $method = 'next_query';
            next HIT;
        }

        # skip weak hits (classical mode)
        next HIT if $hit->hsp_length       < $ARGV_tax_min_len;
        next HIT if $hit->percent_identity < $ARGV_tax_min_ident;
        next HIT if $hit->bit_score        < $ARGV_tax_min_score;

        # fetch hit taxonomy and org
        # optimized code (requires taxon_id|accession seq_ids)
        my $taxon_id = ( split m{\|}xms, $hit->hit_id )[0];

        # k-folds mode (skip hits from current database subset)
        next HIT if $ARGV_kfold && $unwanted{$taxon_id};

        my @taxonomy = $tax->get_taxonomy($taxon_id);

bin/physeter.pl  view on Meta::CPAN

Determine organism taxon based on BLAST infile [default: no].

=item --greedy-taxa

Enable greedy behavior when interpreting the ambiguous taxa provided in the
required argument C<--taxon-list> [default: no].

=item --tax-min-ident=<n>

Minimum identity percentage to consider a hit when computing a LCA [default:
n.default].

=for Euclid: n.type: +number
    n.default: 0

=item --tax-min-len=<n>

Minimum alignment length to consider a hit when computing a LCA [default:
n.default].