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Summary

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

Package variables

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;
}

1;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
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Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://redmine.open-bio.org/projects/bioperl/

Email birney-at-ebi.ac.uk

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