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BioPerl-1.7.8
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::Genewise

NAME

Bio::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:

https://github.com/bioperl/bioperl-live/issues

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