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bin/faeq-seq  view on Meta::CPAN

    -format => 'fasta',
    -fh     => \*STDOUT,
  ) unless ($seq_writer);

  return unless ($seq_objs);

  $seq_writer->write_seq($seq_objs->[0] );
}

#FIXME better statistics
#sub update_stats {
  #my ($seq_objs, $stats, $is_duplicated) = @_;

  #my %tmp_stat;
  #if($is_duplicated) {
    ## count number of duplicated sequences per namespace
    #$tmp_stat
  #}

  #for my $so ( @{$seq_objs} ) {
    #$stats{$so->info->{namespace}} //= { };

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

        my %names;
        for ( my $i = 0; $i < @{$names}; $i++ ) {
            $names{ $names->[$i] } = $i;
        }
        return $self->$orig( \%names );
    } else {
        return $self->$orig;
    }
};

sub update_mark {
    my ( $self, $mark, $from, $to ) = @_;

    $mark = $self->mark_from_name($mark)
        unless ( $mark =~ /^\d+$/ );

    $self->marks->[$mark]->{from} = $from
        if ( $self->marks->[$mark] > $from );

    $self->marks->[$mark]->{to} = $to
        if ( $self->marks->[$mark]->{to} < $to );