Bio::Tools::Primer Feature
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
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Summary
Bio::Tools::Primer::Feature - position of a single primer
Package variables
No package variables defined.
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
new
No description
Code
gc_percent
No description
Code
inversion
No description
Code
Methods description
None available.
Methods code
newdescriptionprevnextTop
sub new {
    my ( $caller, @args) = @_;   
    my ($self) = $caller->SUPER::new(@args); 

    # done - we hope
return $self;
}
gc_percentdescriptionprevnextTop
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;
}
inversiondescriptionprevnextTop
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
FEEDBACKTop
Mailing ListsTop
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
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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.
Reporting BugsTop
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/
AUTHOR - Ewan BirneyTop
Email birney-at-ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _