view release on metacpan or  search on metacpan

lib/Bio/Grep/Backend/BackendI.pm  view on Meta::CPAN

    }
    if ( defined $args->{description} ) {
        open my $NFOFILE, '>', $newfile . '.nfo';
        print ${NFOFILE} $args->{description}
            or $self->_cannot_print("$newfile.nfo");
        close $NFOFILE;
    }
    return;
}

sub _guess_alphabet_of_file {
    my ( $self, $filename ) = @_;
    my $in = Bio::SeqIO->new( -file => $filename );
    return $in->next_seq->alphabet;
}

sub _bioseq_query {
    my ($self) = @_;
    my $query_obj = $self->settings->query;
    my $query;

lib/Bio/Grep/Backend/Vmatch.pm  view on Meta::CPAN

#              Bio::Root::SystemException

sub generate_database {
    my ( $self, @args ) = @_;
    my %args = $self->_prepare_generate_database(@args);

    if ( defined $args{skip} ) {
        return 0;
    }

    my $alphabet = $self->_guess_alphabet_of_file( $args{filename} );
    my $alphabet_specific_arguments = q{};

    my $verbose = q{};
    if ( defined $args{verbose} ) {
        $verbose = ' -v ';
    }

    my $pl = ' -pl ';
    if ( defined $args{prefix_length} ) {
        $pl .= $args{prefix_length} . q{ };