Reference

Bio::Tools::Genomewise(3pm)

Results of one Genomewise run

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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-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    :

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