Bio::Tools Genewise
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Summary
Bio::Tools::Genewise - Results of one Genewise run
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Gene::Exon
Bio::SeqFeature::Gene::GeneStructure
Bio::SeqFeature::Gene::Transcript
Bio::SeqFeature::Generic
Bio::Tools::AnalysisResult
Symbol
Inherit
Bio::Root::IO Bio::Root::Root
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"; } } }
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.
Methods
newDescriptionCode
_get_strandDescriptionCode
_scoreDescriptionCode
_prot_idDescriptionCode
_target_idDescriptionCode
next_predictionDescriptionCode
parsed
No description
Code
_parse_genes
No description
Code
Methods description
newcode    nextTop
 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 Bio::Tools::Genewise
_get_strandcodeprevnextTop
 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
_scorecodeprevnextTop
 Title   : _score
Usage : $obj->_score
Function: get/set for score info
Returns : a score value
_prot_idcodeprevnextTop
 Title   : _prot_id
Usage : $obj->_prot_id
Function: get/set for protein id
Returns :a protein id
_target_idcodeprevnextTop
 Title   : _target_id
Usage : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns :a target id
next_predictioncodeprevnextTop
 Title   : next_prediction
Usage : while($gene = $genewise->next_prediction()) {
# do something
}
Function: Returns the gene structure prediction of the Genewise result
file. Call this method repeatedly until FALSE is returned.
Example : Returns : a Bio::SeqFeature::Gene::GeneStructure object Args :
See Bio::SeqFeature::Gene::GeneStructure
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  $self->_initialize_io(@args);
  return $self;
}
_get_stranddescriptionprevnextTop
sub _get_strand {
  my ($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);
}
_scoredescriptionprevnextTop
sub _score {
    my $self = shift;
    return $self->{'_score'} = shift if @_;
    return $self->{'_score'};
}
_prot_iddescriptionprevnextTop
sub _prot_id {
    my $self = shift;
    return $self->{'_prot_id'} = shift if @_;
    return $self->{'_prot_id'};
}
_target_iddescriptionprevnextTop
sub _target_id {
    my $self = shift;
    return $self->{'_target_id'} = shift if @_;
    return $self->{'_target_id'};
}
next_predictiondescriptionprevnextTop
sub next_prediction {
    my ($self) = @_;

    unless ( $self->parsed ){
	$self->_parse_genes;
	$self->parsed(1);
    }
    return shift @{$self->{'_genes'}};
}
parseddescriptionprevnextTop
sub parsed {
    my $self = shift;
    return $self->{'_parsed'} = 1 if @_ && $_[0]; 
    return $self->{'_parsed'};
}
_parse_genesdescriptionprevnextTop
sub _parse_genes {
    my ($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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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/
AUTHOR - Fugu Team, Jason Stajich Top
 Email: fugui@worf.fugu-sg.org
Email: jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _