| Bio::Tools::Genomewise(3pm) | User Contributed Perl Documentation | Bio::Tools::Genomewise(3pm) |
Bio::Tools::Genomewise - Results of one Genomewise run
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";
}
}
}
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).
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.
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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:
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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 : new
Usage : $obj->new(-file=>"genewise.out");
$obj->new(-fh=>\*GW);
Function: Constructor for genomewise wrapper. Takes either a file or filehandle
Example :
Returns : L<Bio::Tools::Genomewise>
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 : $obj->_target_id Function: get/set for genomic sequence id Example : Returns :a target id
Title : next_prediction
Usage : while($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 :
| 2018-10-27 | perl v5.26.2 |