Bio::Tools::isPcr Bio::Tools::isPcr is a Perl module that can parse isPcr output and make features.
Download

Bio::Tools::isPcr Ranking & Summary

Bio::Tools::isPcr Tags

Perl module perl class bio isPcr parser isPcr tools

Bio::Tools::isPcr Description

Bio::Tools::isPcr is a Perl module that can parse isPcr output and make features. Bio::Tools::isPcr is a Perl module that can parse isPcr output and make features.SYNOPSIS # A simple annotation pipeline wrapper for isPcr data # assuming isPcr data is already generated in file seq1.isPcr # and sequence data is in fasta format in file called seq1.fa # Note: this parser is meant for the default fasta output from # isPcr. bed and psl output formats are not supported. use Bio::Tools::IsPcr; use Bio::SeqIO; my $parser = new Bio::Tools::isPcr(-file => 'seq1.isPcr'); 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 isPcr 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 isPcr data (in the default fasta format), creating a Bio::SeqFeatureI for each isPcr hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation.This module is adapted from the Bio::Tools::EPCR module written by Jason Stajich (jason-at-bioperl.org). Requirements: · Perl

Bio::Tools::isPcr Related Software