Bio-Grep

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

            $rcs = $query->revcom->seq;
        }
        my $result = Bio::Grep::SearchResult->new(
            {   sequence         => $fasta,
                begin            => $upstream,
                end              => $upstream + $fields[$COL_LENGTH],
                alignment        => Bio::SimpleAlign->new(),
                sequence_id      => $internal_seq_id,
                remark           => q{},
                evalue           => $fields[$COL_EVALUE],
                percent_identity => $fields[$COL_IDENTITY],
                query            => Bio::Seq->new(
                    -id   => $query->id,
                    -desc => $query->desc . $rct,
                    -seq  => $rcs,
                ),
            }
        );
        push @results, $result;
    }
    $self->_delete_output();

lib/Bio/Grep/SearchResult.pm  view on Meta::CPAN

use version; our $VERSION = qv('0.10.6');

use IO::String;

use base 'Bio::Root::Root';

use Class::MethodMaker [
    new    => 'new2',
    scalar => [
        qw /sequence query begin end alignment sequence_id remark
            percent_identity evalue dG/
    ],
];

sub new {
    my $self    = shift->new2;
    my $arg_ref = shift;

    #initizialize member variables
    for my $key ( keys %{$arg_ref} ) {
        $self->$key( $arg_ref->{$key} );

lib/Bio/Grep/SearchResult.pm  view on Meta::CPAN

hash reference that initializes the member variables below.

Only called by the back-end parser. 

    my $result = Bio::Grep::SearchResult->new(
        {   sequence         => $seq,
            begin            => $begin,
            end              => $end,
            alignment        => $alignment,
            ...
            percent_identity => $identity,
        }
    );

=back

=head2 PACKAGE METHODS

=over 

=item C<subject()>

lib/Bio/Grep/SearchResult.pm  view on Meta::CPAN

Get/set C<dG> . See L<Bio::Grep::RNA::HybridizationI> for details.

=item C<remark()>

Get/set some additional information like filter results to this hit.

=item C<evalue()>

Get/set the evalue of this hit.

=item C<percent_identity()>

Get/set the identity in percent of this hit. 

=back

=head1 SEE ALSO

L<Bio::SimpleAlign> 
L<Bio::LocatableSeq> 
L<Bio::AlignIO> 
L<Bio::Seq>
L<Bio::SeqIO>