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Summary

Bio::Tools::EPCR - Parse ePCR output and make features

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root Bio::SeqAnalysisParserI

Synopsis

    # A simple annotation pipeline wrapper for ePCR data
    # assuming ePCR data is already generated in file seq1.epcr
    # and sequence data is in fasta format in file called seq1.fa

    use Bio::Tools::EPCR;
    use Bio::SeqIO;
    my $parser = new Bio::Tools::EPCR(-file => 'seq1.epcr');
    my $seqio = new Bio::SeqIO(-format => 'fasta', -file => 'seq1.fa');
    my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO");

    while( my $feat = $parser->next_feature ) {
	# add EPCR annotation to a sequence
	$seq->add_SeqFeature($feat);
    }
    my $seqout = new Bio::SeqIO(-format => 'embl');
    $seqout->write_seq($seq);

Description

This object serves as a parser for ePCR data, creating a
Bio::SeqFeatureI for each ePCR hit. These can be processed or added
as annotation to an existing Bio::SeqI object for the purposes of
automated annotation.

Methods

Methods description

 Title   : new
 Usage   : my $epcr = new Bio::Tools::EPCR(-file => $file);
 Function: Initializes a new EPCR parser
 Returns : Bio::Tools::EPCR
 Args    : -fh   => filehandle
           OR
           -file => filename

 Title   : next_feature
 Usage   : $seqfeature = $obj->next_feature();
 Function: Returns the next feature available in the analysis result, or
           undef if there are no more features.
 Example :
 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
           more features.
 Args    : none

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  $self->_initialize_io(@args);
  
  return $self;

}

sub next_feature {

    my ($self) = @_;
    my $line = $self->_readline;
    return undef unless defined($line);
    chomp($line);
    my($seqname,$location,$mkrname, $rest) = split(/\s+/,$line,4);
    
    my ($start,$end) = ($location =~ /(\S+)\.\.(\S+)/);

    # If we require that e-PCR is run with D=1 we can detect a strand
    # for now hardcoded to 0

    my $strand = 0;
    my $markerfeature = new Bio::SeqFeature::Generic ( '-start'   => $start,
						       '-end'     => $end,
						       '-strand'  => $strand,
						       '-source'  => 'e-PCR',
						       '-primary' => 'sts',
						       '-seq_id'  => $seqname,
						       '-tag'     => {
							   'name'=> $mkrname,
							   'note'=> $rest,
						       });
    return $markerfeature;
}

1;

}

General documentation

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