NAME

Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature->primary_tag

SYNOPSIS

  use Bio::SeqIO;
  use Bio::SeqFeature::Tools::TypeMapper;

  # first fetch a genbank SeqI object
  $seqio =
    Bio::SeqIO->new(-file=>'AE003644.gbk',
                    -format=>'GenBank');
  $seq = $seqio->next_seq();

  $tm = Bio::SeqFeature::Tools::TypeMapper->new;

  # map all the types in the sequence
  $tm->map_types(-seq=>$seq,
                 {CDS=>'ORF',
                  variation=>sub {
                      my $f = shift;
                      $f->length > 1 ?
                        'variation' : 'SNP'
                  },
                 });

   # alternatively, use the hardcoded SO mapping
   $tm->map_types_to_SO(-seq=>$seq);

DESCRIPTION

This class implements an object for mapping between types; for example, the types in a genbank feature table, and the types specified in the Sequence Ontology.

You can specify your own mapping, either as a simple hash index, or by providing your own subroutines.

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 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://bugzilla.bioperl.org/

AUTHOR - Chris Mungall

Email: cjm@fruitfly.org

APPENDIX

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

new

 Title   : new
 Usage   : $unflattener = Bio::SeqFeature::Tools::TypeMapper->new();
 Function: constructor
 Example : 
 Returns : a new Bio::SeqFeature::Tools::TypeMapper
 Args    : see below

typemap

 Title   : typemap
 Usage   : $obj->typemap($newval)
 Function: 
 Example : 
 Returns : value of typemap (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

map_types

 Title   : map_types
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

map_types_to_SO

 Title   : map_types_to_SO
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

hardcodes the genbank to SO mapping

Based on revision 1.22 of SO

Please see the actual code for the mappings

!!!NOT COMPLETE!!!