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.
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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 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
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.