Ewan Birney

NAME

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

SYNOPSIS

   $Genemark = Bio::Tools::Genemark->new(-file => 'result.Genemark');
   # filehandle:
   $Genemark = Bio::Tools::Genemark->new( -fh  => \*INPUT );

   # parse the results
   # note: this class is-a Bio::Tools::AnalysisResult which implements
   # Bio::SeqAnalysisParserI, i.e., $Genemark->next_feature() is the same
   while($gene = $Genemark->next_prediction()) {
       # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
       # off Bio::SeqFeature::Gene::Transcript.
       #
       # $gene->exons() returns an array of 
       # Bio::Tools::Prediction::Exon objects
       # all exons:
       @exon_arr = $gene->exons();

       # initial exons only
       @init_exons = $gene->exons('Initial');
       # internal exons only
       @intrl_exons = $gene->exons('Internal');
       # terminal exons only
       @term_exons = $gene->exons('Terminal');
       # singleton exons: 
       ($single_exon) = $gene->exons();
   }

   # essential if you gave a filename at initialization (otherwise the file
   # will stay open)
   $Genemark->close();

DESCRIPTION

The Genemark module provides a parser for Genemark gene structure prediction output. It parses one gene prediction into a Bio::SeqFeature::Gene::Transcript- derived object.

This module has been developed around genemark.hmm for eukaryots v2.2a and will probably not work with other versions.

This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits. See Bio::SeqAnalysisParserI.

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://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Hilmar Lapp, Mark Fiers

Email hlapp@gmx.net m.w.e.j.fiers@plant.wag-ur.nl

Describe contact details here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

analysis_method

 Usage     : $Genemark->analysis_method();
 Purpose   : Inherited method. Overridden to ensure that the name matches
             /GeneMark.hmm/i.
 Returns   : String
 Argument  : n/a

next_feature

 Title   : next_feature
 Usage   : while($gene = $Genemark->next_feature()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the Genemark result
           file. Call this method repeatedly until FALSE is returned.

           The returned object is actually a SeqFeatureI implementing object.
           This method is required for classes implementing the
           SeqAnalysisParserI interface, and is merely an alias for 
           next_prediction() at present.

 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

next_prediction

 Title   : next_prediction
 Usage   : while($gene = $Genemark->next_prediction()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the Genemark result
           file. Call this method repeatedly until FALSE is returned.

 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

_parse_predictions

 Title   : _parse_predictions()
 Usage   : $obj->_parse_predictions()
 Function: Parses the prediction section. Automatically called by
           next_prediction() if not yet done.
 Example :
 Returns : 

_prediction

 Title   : _prediction()
 Usage   : $gene = $obj->_prediction()
 Function: internal
 Example :
 Returns : 

_add_prediction

 Title   : _add_prediction()
 Usage   : $obj->_add_prediction($gene)
 Function: internal
 Example :
 Returns : 

_predictions_parsed

 Title   : _predictions_parsed
 Usage   : $obj->_predictions_parsed
 Function: internal
 Example :
 Returns : TRUE or FALSE

_has_cds

 Title   : _has_cds()
 Usage   : $obj->_has_cds()
 Function: Whether or not the result contains the predicted CDSs, too.
 Example :
 Returns : TRUE or FALSE

_read_fasta_seq

 Title   : _read_fasta_seq()
 Usage   : ($id,$seqstr) = $obj->_read_fasta_seq();
 Function: Simple but specialised FASTA format sequence reader. Uses
           $self->_readline() to retrieve input, and is able to strip off
           the traling description lines.
 Example :
 Returns : An array of two elements.