Bio::Tools
Genomewise
Toolbar
Summary
Bio::Tools::Genomewise - Results of one Genomewise run
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Tools::Genomewise;
my $gw = Bio::Tools::Genomewise(-file=>"genomewise.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. You will need to specify
the proper target sequence id on the object with the
$feature->seq_id($seqid).
Methods
Methods description
Title : new
Usage : $obj->new(-file=>"genewise.out");
$obj->new(-fh=>\*GW);
Function: Constructor for genomewise wrapper. Takes either a file or filehandle
Example :
Returns : Bio::Tools::Genomewise |
Title : next_prediction
Usage : while($gene = $genewise->next_prediction()) {
# do something
}
Function: Returns the gene structure prediction of the Genomewise result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : a Bio::SeqFeature::Gene::GeneStructure object
Args : |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
return $self; } | sub next_prediction
{ my ($self) = @_;
my $genes;
while ($_ = $self->_readline) {
$self->debug( $_ );
last if m{^//};
if( /^Gene\s+\d+\s*$/ ) {
$genes = Bio::SeqFeature::Gene::GeneStructure->new
(-source => $Srctag,
-seq_id => $self->_target_id,
);
$_ = $self->_readline;
$self->debug( $_ );
unless ( /^Gene\s+(\d+)\s+(\d+)\s*$/ ) {
$self->warn("Unparseable genomewise output");
last;
}
my $transcript = Bio::SeqFeature::Gene::Transcript->new
(-source => $Srctag,
-seq_id => $self->_target_id,
-start => $1,
-end => $2,
);
my $nbr = 1;
while( $_ = $self->_readline ) {
$self->debug( $_ );
unless( m/^\s+Exon\s+(\d+)\s+(\d+)\s+phase\s+(\d+)/ ){
$self->_pushback($_);
last;
}
my ($e_start,$e_end,$phase,$e_strand) = ($1,$2,$3);
($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 => $Srctag,
-start=>$e_start,
-end=>$e_end,
-frame => $phase,
-strand=>$e_strand);
$exon->add_tag_value("Exon",$nbr++);
$exon->add_tag_value('phase',$phase);
$transcript->add_exon($exon);
}
$genes->add_transcript($transcript);
last;
}
}
return $genes;
}
1;} | General documentation
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
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.
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-at-worf.fugu-sg.org
jason-at-bioperl-dot-org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : score
Usage : $obj->score
Function: get/set for score info
Example :
Returns : a score value
Title : _prot_id
Usage : $obj->_prot_id
Function: get/set for protein id
Example :
Returns :a protein id
Title : _target_id
Usage : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns :a target id