Bio::Tools::tRNAscanSE.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output

SYNOPSIS

    use Bio::Tools::tRNAscanSE;
 
    my $parser = Bio::Tools::tRNAscanSE->new(-file => 'result.tRNAscanSE');
 
    # parse the results
    while( my $gene = $parser->next_prediction ) {
 
        @exon_arr = $gene->get_SeqFeatures();
 
    }
 
 

DESCRIPTION

This script will parse tRNAscan-SE output. Just the tabular output of the tRNA locations in the genome for now.

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

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

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::tRNAscanSE->new();
  Function: Builds a new Bio::Tools::tRNAscanSE object 
  Returns : an instance of Bio::Tools::tRNAscanSE
  Args    : -fh/-file for input filename
            -genetag => primary tag used in gene features (default 'tRNA_gene')
            -exontag => primary tag used in exon features (default 'tRNA_exon')
            -srctag  => source tag used in all features (default 'tRNAscan-SE')
 
 

gene_tag

  Title   : gene_tag
  Usage   : $obj->gene_tag($newval)
  Function: Get/Set the value used for the 'gene_tag' of genes
            Default is 'tRNA_gene' as set by the global $GeneTag
  Returns : value of gene_tag (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

source_tag

  Title   : source_tag
  Usage   : $obj->source_tag($newval)
  Function: Get/Set the value used for the 'source_tag' of exons and genes
            Default is 'tRNAscan-SE' as set by the global $SrcTag
  Returns : value of source_tag (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

exon_tag

  Title   : exon_tag
  Usage   : $obj->exon_tag($newval)
  Function: Get/Set the value used for the 'primary_tag' of exons
            Default is 'tRNA_exon' as set by the global $ExonTag
  Returns : value of exon_tag (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

analysis_method

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

next_feature

  Title   : next_feature
  Usage   : while($gene = $genscan->next_feature()) {
                   # do something
            }
  Function: Returns the next gene structure prediction of the Genscan 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::SeqFeature::Generic object.
  Args    :
 See also : L<Bio::SeqFeature::Generic>
 
 

next_prediction

  Title   : next_prediction
  Usage   : while($gene = $genscan->next_prediction()) {
                   # do something
            }
  Function: Returns the next gene structure prediction of the Genscan result
            file. Call this method repeatedly until FALSE is returned.
 
  Example :
  Returns : A Bio::SeqFeature::Generic object.
  Args    :
 See also : L<Bio::SeqFeature::Generic>