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bin/facompare  view on Meta::CPAN

my $only_header;

GetOptions( 'only-header|oh|o' => \$only_header ) or die "Fehler im System";

my ( $file1, $file2 ) = @ARGV;
die "$file1 is no file" unless ( -f $file1 );
die "$file2 is no file" unless ( -f $file2 );

my $first_file_in_mem;
my ( $load_in_memory, $from_disk );
if ( stat($file1)->size > stat($file2)->size ) {
    $load_in_memory = $file2;
    $from_disk      = $file1;
} else {
    $load_in_memory    = $file1;
    $first_file_in_mem = 1;
    $from_disk         = $file2;
}

my %memory_seq;
{

lib/Bio/Gonzales/Domain/Identification/HMMER.pm  view on Meta::CPAN

    $cache->close;

    return \%result_for_sequence;
}

sub _create_cache_string {
    my ( $self, $sequence_file, $k ) = @_;

    return join "\t",
        (
        _basename_no_suffix($sequence_file) . "_" . stat($sequence_file)->size,
        $k->{seq_id}, $k->{hmm_acc}, $k->{hmm_score}, $k->{from}, $k->{to}
        );
}

sub _update_sequence_mark {
    my ( $self, $seq_result, $best_hit ) = @_;

    my @domain_groups = @{ $self->domain_groups };

    for ( my $i = 0; $i < @domain_groups; $i++ ) {

lib/Bio/Gonzales/Domain/Identification/HMMER.pm  view on Meta::CPAN

            keys %{ $domain_groups[$i] }
            );
    }
}

sub _get_cached_hits {
    my ( $self, $sequence_file ) = @_;

    my @best_hits;

    my $seq_file_id = _basename_no_suffix($sequence_file) . "_" . stat($sequence_file)->size;

    open my $cache, '<', $self->discovered_cache_file
        or croak "Can't open filehandle: $!";
    while ( my $l = <$cache> ) {
        my @rows = split /\t/, $l;
        push @best_hits,
            {
            seq_id    => $rows[1],
            hmm_acc   => $rows[2],
            hmm_score => $rows[3],