#
# BioPerl module for Bio::Tools::Genewise
#
# Copyright Fugu Team
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Genewise - Results of one Genewise run
=head1 SYNOPSIS
use Bio::Tools::Genewise;
my $gw = Bio::Tools::Genewise(-file=>"genewise.out");
while (my $gene = $gw->next_prediction){
my @transcripts = $gene->transcripts;
foreach my $t(@transcripts){
my @exons = $t->exons;
foreach my $e(@exons){
print $e->start." ".$e->end."\n";
}
}
}
=head1 DESCRIPTION
This is the parser for the output of Genewise. It takes either a file
handle or a file name and returns a
Bio::SeqFeature::Gene::GeneStructure object.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Fugu Team, Jason Stajich
Email: fugui@worf.fugu-sg.org
Email: jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Genewise;
use vars qw($Srctag);
use strict;
use Symbol;
use Bio::Tools::AnalysisResult;
use Bio::SeqFeature::Generic;
use Bio::SeqFeature::Gene::Exon;
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Gene::Transcript;
use Bio::SeqFeature::Gene::GeneStructure;
use base qw(Bio::Root::Root Bio::Root::IO);
$Srctag = 'genewise';
=head2 new
Title : new
Usage : $obj->new(-file=>"genewise.out");
$obj->new(-fh=>\*GW);
Function: Constructor for genewise wrapper. Takes either a file or filehandle
Example :
Returns : Bio::Tools::Genewise object
See L<Bio::Tools::Genewise>
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize_io(@args);
return $self;
}
=head2 _get_strand
Title : _get_strand
Usage : $obj->_get_strand
Function: takes start and end values, swap them if start>end and
returns end
Example :
Returns :$start,$end,$strand
=cut
sub _get_strand {
my ($self,$start,$end) = @_;
defined($start) || $self->throw("Need a start");
defined($end) || $self->throw("Need an end");
my $strand;
if ($start > $end) {
my $tmp = $start;
$start = $end;
$end = $tmp;
$strand = -1;
}
else {
$strand = 1;
}
return ($start,$end,$strand);
}
=head2 _score
Title : _score
Usage : $obj->_score
Function: get/set for score info
Returns : a score value
=cut
sub _score {
my $self = shift;
return $self->{'_score'} = shift if @_;
return $self->{'_score'};
}
=head2 _prot_id
Title : _prot_id
Usage : $obj->_prot_id
Function: get/set for protein id
Returns :a protein id
=cut
sub _prot_id {
my $self = shift;
return $self->{'_prot_id'} = shift if @_;
return $self->{'_prot_id'};
}
=head2 _target_id
Title : _target_id
Usage : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns :a target id
=cut
sub _target_id {
my $self = shift;
return $self->{'_target_id'} = shift if @_;
return $self->{'_target_id'};
}
=head2 next_prediction
Title : next_prediction
Usage : while($gene = $genewise->next_prediction()) {
# do something
}
Function: Returns the gene structure prediction of the Genewise result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : a Bio::SeqFeature::Gene::GeneStructure object
Args :
See L<Bio::SeqFeature::Gene::GeneStructure>
=cut
sub next_prediction {
my ($self) = @_;
unless ( $self->parsed ){
$self->_parse_genes;
$self->parsed(1);
}
return shift @{$self->{'_genes'}};
}
sub parsed {
my $self = shift;
return $self->{'_parsed'} = 1 if @_ && $_[0];
return $self->{'_parsed'};
}
sub _parse_genes {
my ($self) = @_;
my (@alignments,@genes);
local ($/) = "//";
while ( defined($_ = $self->_readline) ) {
$self->debug( $_ );
while( /Alignment\s+(\d+)\s+Score\s+(\S+)\s+\(Bits\)/g ) {
$alignments[$1] = $2;
}
if( /Score\s+(\-?\d+(\.\d+)?)/ ) {
$self->_score($1);# unless defined $self->_score;
}
if( /Query\s+(?:protein|model)\:\s+(\S+)/ ) {
$self->_prot_id($1); #unless defined $self->_prot_id;
}
if( /Target Sequence\s+(\S+)/ ) {
$self->_target_id($1);# unless defined $self->_target_id;
}
next unless /Gene\s+\d+\n/;
my @genes_txt = split(/Gene\s+\d+\n/,$_);
shift @genes_txt; #remove first empty entry
my $gene_num = 1;
foreach my $gene_txt (@genes_txt) {
my $score = $alignments[$gene_num];
# If genewise has assigned a strand to the gene as a whole
# overall gene start and end
my ($g_start, $g_end, $type) =
$gene_txt =~ m/Gene\s+
(\d+)[\s-]+ # start (1-based)
(\d+)\s+ # end
(?:\[(\w+)\])? #
/x;
my $g_strand;
my $source_tag = $type ? "$Srctag". "_$type" : $Srctag;
my $genes = Bio::SeqFeature::Gene::GeneStructure->new
(-source => $source_tag,
-score => $self->_score,
);
$genes->add_tag_value('ID', $self->_prot_id.".gene");
my $transcript = Bio::SeqFeature::Gene::Transcript->new
(-source => $source_tag,
-score => $score);
($g_start, $g_end, $g_strand) = $self->_get_strand($g_start,$g_end);
$genes->strand($g_strand);
# grab exon + supporting feature info
my @exons;
unless ( @exons = $gene_txt =~ m/(Exon .+\s+Supporting .+)/g ) {
@exons = $gene_txt =~ m/(Exon .+\s+)/g;
}
my $nbr = 1;
# loop through each exon-supporting feature pair
foreach my $e (@exons){
my ($e_start,$e_end,$phase) =
$e =~ m/Exon\s+
(\d+)[\s-]+ # start (1 based)
(\d+)\s+ # end
phase\s+(\d+) # phase
/x;
my $e_strand;
($e_start,$e_end,$e_strand) = $self->_get_strand($e_start,
$e_end);
$transcript->strand($e_strand) unless $transcript->strand != 0;
my $exon = Bio::SeqFeature::Gene::Exon->new
(-seq_id =>$self->_target_id,
-source => $source_tag,
-start =>$e_start,
-end =>$e_end,
-score => $score,
#-frame => $phase,
-strand =>$e_strand);
$exon->add_tag_value('phase',$phase);
$exon->is_coding(1);
if( $self->_prot_id ) {
$exon->add_tag_value('Parent',$self->_prot_id);
}
$exon->add_tag_value("Exon",$nbr++);
if( $e =~ m/Supporting\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)/) {
my ($geno_start,$geno_end,
$prot_start, $prot_end) = ($1,$2,$3,$4);
my $prot_strand;
($prot_start,$prot_end,
$prot_strand) = $self->_get_strand($prot_start,$prot_end);
my $pf = Bio::SeqFeature::Generic->new
( -start => $prot_start,
-end => $prot_end,
-seq_id => $self->_prot_id,
-score => $score,
-strand => $prot_strand,
-source => $source_tag,
-primary_tag => 'supporting_protein_feature',);
my $geno_strand;
($geno_start,$geno_end,
$geno_strand) = $self->_get_strand($geno_start,$geno_end);
my $gf = Bio::SeqFeature::Generic->new
( -start => $geno_start,
-end => $geno_end,
-seq_id => $self->_target_id,
-score => $score,
-strand => $geno_strand,
-source => $source_tag,
-primary_tag => 'supporting_genomic_feature',);
my $fp = Bio::SeqFeature::FeaturePair->new
(-feature1 =>$gf,
-feature2 =>$pf);
$exon->add_tag_value( 'supporting_feature',$fp );
if( $self->_prot_id ) {
$exon->add_tag_value('Target','Protein:'.$self->_prot_id);
$exon->add_tag_value('Target',$prot_start);
$exon->add_tag_value('Target',$prot_end);
}
}
$transcript->add_exon($exon);
}
$transcript->seq_id($self->_target_id);
$transcript->add_tag_value('ID', $self->_prot_id);
$transcript->add_tag_value('Parent', $self->_prot_id.".gene");
$genes->add_transcript($transcript);
$genes->seq_id($self->_target_id);
push @genes, $genes;
$gene_num++;
}
}
$self->{'_genes'} = \@genes;
}
1;