Bio-MUST-Apps-Physeter

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bin/physeter.pl  view on Meta::CPAN

            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);
        # regular code (more general)
#       my @taxonomy = $tax->get_taxonomy_from_seq_id( $hit->hit_id );
        my $hit_org = $taxonomy[-1];

        # skip self hits (corresponding to query_org)



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