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


    # 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
    my $seqout = new Bio::SeqIO(-format => 'embl');


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.


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


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