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 $seq->add_SeqFeature($feat); } my $seqout = new Bio::SeqIO(-format => 'embl'); $seqout->write_seq($seq); 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.

Mailing Lists
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Reporting Bugs
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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org Describe contact details here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
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

next_feature
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