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://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 - Hilmar Lapp, Mark Fiers

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

APPENDIX

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

new

Title   : new
Usage   : my $obj = Bio::Tools::Genemark->new();
Function: Builds a new Bio::Tools::Genemark object
Returns : an instance of Bio::Tools::Genemark
Args    : seqname

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.

_seqname

Title   : _seqname
Usage   : $obj->_seqname($seqname)
Function: internal
Example :
Returns : String

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq