Bio::Tools::Genewise - 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.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email: fugui@worf.fugu-sg.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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 : L<Bio::Tools::Genewise>

_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

_score
Title : _score Usage : $obj->_score Function: get/set for score info Returns : a score value

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

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

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 :