Bio::Tools::Genewise(3) Results of one Genewise run


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";


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.


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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : $obj->new(-file=>"genewise.out");
 Function: Constructor for genewise wrapper. Takes either a file or filehandle
 Example :
 Returns : Bio::Tools::Genewise object

See Bio::Tools::Genewise


 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
 Returns : a score value


 Title   : _prot_id
 Usage   : $obj->_prot_id
 Function: get/set for protein id 
 Returns :a protein id


 Title   : _target_id
 Usage   : $obj->_target_id
 Function: get/set for genomic sequence id
 Example :
 Returns :a target id


 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