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lib/Bio/Tools/Hmmpfam.pm  view on Meta::CPAN

            $feature{score} = $feature{p_value};
            $feature{start} = $start;
            $feature{end} = $end;
            $feature{hname} = $hid;
            $feature{hstart} = $hstart;
            $feature{hend} = $hend;
            ($feature{source}) = 'pfam';
            $feature{primary} = $hid;
            ($feature{program}) = 'pfam';
            ($feature{db}) = 'db1';
            ($feature{logic_name}) = 'hmmpfam';
            my $new_feat = $self->create_feature (\%feature);
            return $new_feat

        }
        next;

    }
    return;
}

=head2 create_feature

 Title   : create_feature
 Usage   : my $feat=$hmmpfam_parser->create_feature($feature,$seqname)
 Function: creates a SeqFeature Generic object
 Returns : L<Bio::SeqFeature::Generic>
 Args    :


=cut

sub create_feature {
    my ($self, $feat) = @_;



    my $feature1= Bio::SeqFeature::Generic->new( -seq_id  =>$feat->{name},
                                                -start      =>$feat->{start},
                                                -end        =>$feat->{end},
                                                -score      =>$feat->{score},
                                                -source     =>$feat->{source},
                                                -primary    =>$feat->{primary},
                                                   );



    my $feature2= Bio::SeqFeature::Generic->new(
                                                 -start      =>$feat->{hstart},
                                                 -end        =>$feat->{hend},
                                                  );




    my $featurepair = Bio::SeqFeature::FeaturePair->new;
    $featurepair->feature1 ($feature1);
    $featurepair->feature2 ($feature2);

   $featurepair->add_tag_value('evalue',$feat->{p_value});
   $featurepair->add_tag_value('percent_id','NULL');
   $featurepair->add_tag_value("hid",$feat->{primary});
    return  $featurepair;

}

=head2 seqname

 Title   :   seqname
 Usage   :   obj->seqname($seqname)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :   seqname

=cut

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

    if(defined($seqname))
    {
        $self->{'seqname'}=$seqname;
    }

    return $self->{'seqname'};

}

1;