Summary

Bio::Tools::Primer::Feature - position of a single primer

Package variables

Included modules

Inherit

Bio::SeqFeature::Generic

Synopsis

    use Bio::Tools::Primer::Feature;

    my $pf = Bio::Tools::Primer::Feature->new( -start => $start, -end => $end, -strand => $strand);
    $pf->attach_seq($seq);

    # is a SeqFeatureI

    print "primer starts at ",$pf->start," with sequence ",$pf->seq->seq(),"\n";

    # helper functions

    print "GC percentage ",$pf->gc(),"\n";
    print "has inversion of size 4 at ",$pf->inversion(4),"\n";

Description

Primer Features represents one primer in a primer pair. This object is mainly for
designing primers, and probably principly used in the primer design system

Methods

Methods description

None available.

Methods code

sub new {

    my ( $caller, @args) = @_;   
    my ($self) = $caller->SUPER::new(@args); 

    # done - we hope
    return $self;

}

sub gc_percent {

    my $self = shift;

    my $seq = $self->seq();

    if( !defined $seq ) {
	$self->throw("Primer feature has no attached sequence, can't calculate GC");
    }

    my $str = $seq->seq();

    my $count = $str =~ tr/GCgc/GCgc/;

    return $count*100.0 / $seq->length;

}

sub inversion {

    my $self = shift;
    my $size = shift;

    if( !defined $size ) {
	$self->throw("Must have size paramter in inversion");
    }

    my $seq = $self->seq();

    if( !defined $seq ) {
	$self->throw("Primer feature has no attached sequence, can't calculate inversion");
    }

    my $len = $seq->length - $size;

    my $str = $seq->seq();

    foreach my $i ( 0 .. $len ) {
	my $revstr = substr($str,$i,$size);
	my $orig = $revstr;
	$revstr = reverse $revstr;
	$revstr = s/[^ATGCNatgcn]/N/g;

	$revstr =~ tr/ATGCNatgcn/TACGNtacgn/;

	if( $str =~ /$revstr/ ) {
	    return $orig;
	}
    }

    return undef;

}

General documentation

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Email birney@ebi.ac.uk
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Additional contributors names and emails here

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _