Bio::Tools::Genewise(3User Contributed Perl DocumentatiBio::Tools::Genewise(3)NAMEBio::Tools::Genewise - Results of one Genewise run
SYNOPSIS
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";
}
}
}
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.
FEEDBACK
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
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.
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 the
web:
http://bugzilla.open-bio.org/
AUTHOR - Fugu Team, Jason Stajich
Email: fugui@worf.fugu-sg.org
Email: jason-at-bioperl.org
APPENDIX
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 : Bio::Tools::Genewise object
See 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 :
See Bio::SeqFeature::Gene::GeneStructure
perl v5.14.1 2011-07-22 Bio::Tools::Genewise(3)
