Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Tools::Glimmer.3pm

NAME

Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions

SYNOPSIS

    use Bio::Tools::Glimmer;
 
    # file
    my $parser = Bio::Tools::Glimmer->new(-file => $file);
    # filehandle:
    $parser = Bio::Tools::Glimmer->new( -fh  => \*INPUT );
    # provide a sequence identifier (Glimmer 2.X)
    my $parser = Bio::Tools::Glimmer->new(-file => $file, -seqname => seqname);
    # force format (override automatic detection)
    my $parser = Bio::Tools::Glimmer->new(-file => $file, -format => 'GlimmerM');
 
    # parse the results
    # note: this class is-a Bio::Tools::AnalysisResult which implements
    # Bio::SeqAnalysisParserI, i.e., $glimmer->next_feature() is the same
 
    while(my $gene = $parser->next_prediction()) {
        # For eukaryotic input (GlimmerM/GlimmerHMM), $gene will be an instance
        # of Bio::Tools::Prediction::Gene, which inherits off
        # Bio::SeqFeature::Gene::Transcript, and $gene->exons() will return an
        # array of Bio::Tools::Prediction::Exon objects.
        # For prokaryotic input (Glimmer2.X/Glimmer3.X), $gene will be an
        # instance of Bio::SeqFeature::Generic
 
        # all exons (eukaryotic only):
        @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');
    }
 
 

DESCRIPTION

This is a module for parsing Glimmer, GlimmerM and GlimmerHMM predictions. It will create gene objects from the prediction report which can be attached to a sequence using Bioperl objects, or output as GFF suitable for loading into Bio::DB::GFF for use with Gbrowse.

Glimmer is open source and available at <http://www.cbcb.umd.edu/software/glimmer/>.

GlimmerM is open source and available at <http://www.tigr.org/software/glimmerm/>.

GlimmerHMM is open source and available at <http://www.cbcb.umd.edu/software/GlimmerHMM/>.

Note that Glimmer 2.X will only process the first sequence in a fasta file, and the prediction report does not contain any sort of sequence identifier

Note that Glimmer 3.X produces two output files. This module only parses the .predict file.

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via email or the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

CONTRIBUTORS

Torsten Seemann

Mark Johnson

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::Glimmer->new();
  Function: Builds a new Bio::Tools::Glimmer object 
  Returns : an instance of Bio::Tools::Glimmer
  Args    : format ('Glimmer', 'GlimmerM', 'GlimmerHMM'), seqname
 
 

analysis_method

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

next_feature

  Title   : next_feature
  Usage   : while($gene = $glimmer->next_feature()) {
                   # do something
            }
  Function: Returns the next gene structure prediction of the Glimmer 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 = $glimmer->next_prediction()) {
                   # do something
            }
  Function: Returns the next gene structure prediction of the Glimmer 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 :
 
 

_parse_eukaryotic

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

_parse_prokaryotic

  Title   : _parse_prokaryotic()
  Usage   : $obj->_parse_prokaryotic()
  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
 
 

_seqname

  Title   : _seqname
  Usage   : $obj->_seqname($seqname)
  Function: internal (for Glimmer 2.X)
  Example :
  Returns : String
 
 

_seqlength

  Title   : _seqlength
  Usage   : $obj->_seqlength($seqlength)
  Function: internal (for Glimmer 2.X)
  Example :
  Returns : String
 
 

_format

  Title   : _format
  Usage   : $obj->_format($format)
  Function: internal
  Example :
  Returns : String
 
 

_detail_file

  Title   : _detail_file
  Usage   : $obj->_detail_file($filename)
  Function: internal (for Glimmer 3.X)
  Example :
  Returns : String