NAME

Bio::Tools::Genomewise - Results of one Genomewise run

SYNOPSIS

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";
      }
    }
}

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. You will need to specify the proper target sequence id on the object with the $feature->seq_id($seqid).

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Fugu Team, Jason Stajich

Email: fugui-at-worf.fugu-sg.org
       jason-at-bioperl-dot-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 genomewise wrapper. Takes either a file or filehandle
Example :
Returns : L<Bio::Tools::Genomewise>

_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
Example :
Returns : a score value

_prot_id

Title   : _prot_id
Usage   : $obj->_prot_id
Function: get/set for protein id 
Example :
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 Genomewise result
          file. Call this method repeatedly until FALSE is returned.

Example :
Returns : a Bio::SeqFeature::Gene::GeneStructure object
Args    :

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq