Bio::Tools::ipcress Bio::Tools::ipcress is a Perl module that can parse ipcress output and make features.
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Perl module perl class bio ipcress parser ipcress tools

Bio::Tools::ipcress Description

Bio::Tools::ipcress is a Perl module that can parse ipcress output and make features. Bio::Tools::ipcress is a Perl module that can parse ipcress output and make features.SYNOPSIS # A simple annotation pipeline wrapper for ipcress data # assuming ipcress data is already generated in file seq1.ipcress # and sequence data is in fasta format in file called seq1.fa use Bio::Tools::ipcress; use Bio::SeqIO; my $parser = new Bio::Tools::ipcress(-file => 'seq1.ipcress'); 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 ipcress 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 ipcress data, creating a Bio::SeqFeatureI for each ipcress 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).Ipcress is available through Guy Slater's Exonerate package http://www.ebi.ac.uk/~guy/exonerate/ Requirements: · Perl

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