| Bio::Tools::Genewise(3pm) | User Contributed Perl Documentation | Bio::Tools::Genewise(3pm) |
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.
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://github.com/bioperl/bioperl-live/issues
Email: fugui@worf.fugu-sg.org Email: jason-at-bioperl.org
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");
$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
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
| 2021-08-15 | perl v5.32.1 |