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lib/Bio/MUST/Apps/OmpaPa/Roles/Parsable.pm  view on Meta::CPAN

                                ->name( $file . '*.json' )
                                ->in( $self->file->dir );
    my @sorted = nsort( @files );

    # because File::Find::Rule goes recursively in directories
    # use the directory of entry file
    my @finalsort;

    FINALSORT:
    for my $f (@sorted) {
        my @parts = split m{/}xms, $f;
        if ("$parts[0]/" eq $dir) {
            push @finalsort, $f;
            next FINALSORT;
        }
        push @finalsort, $f if @parts < 2;
    }

    return file( $finalsort[-1] );
}

lib/Bio/MUST/Apps/OmpaPa/Roles/Parsable.pm  view on Meta::CPAN

}

sub _build_coeffs {
    my $self = shift;

    my %count_for;
    my %coeffs_for;

    for my $hit ($self->all_hits) {
        # TODO: use SeqId methods: $_->$method // $_->taxon_id
        my $org = (split m{\|}xms, $hit->{acc})[0];
        $count_for{$org}++;

        my $coeff_len = $hit->{len} / $hit->{qlen};
        my $coeff_hmm
            = ( $hit->{hmm_to} - $hit->{hmm_from} + 1 ) / $hit->{qlen};

        my ($index, $label) = $self->scheme
            ? $self->scheme->icol( $hit->{acc} ) : (undef, undef);
        unless (defined $index) {
            $index = 0;

lib/Bio/MUST/Apps/OmpaPa/Roles/Parsable.pm  view on Meta::CPAN

        qlen        => $qlen
    );

    return \%return;
}

sub _org_col {
    my $self = shift;

    my @ids = map { $_->{acc} } $self->all_hits;
    my @orgs = map { (split m{\|}xms, $_)[0] } @ids;
    my %count_orgs;

    for my $org (@orgs) {
        $count_orgs{$org}++;
    }

    my $nb_org_tot = keys %count_orgs;
    my $max = (sort {$a <=> $b} values %count_orgs)[$nb_org_tot-1];
    my $color_n = $max;         # range scale palette
    # limit coloration: 3 (default) or more times the same organism in yellow