Provided by: libbio-perl-perl_1.7.2-3_all bug

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://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://github.com/bioperl/bioperl-live/issues

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    :

        dgg: added -undefined => "region" option to produce all valid SO mappings.

   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

       Taken from

       <http://sequenceontology.org/resources/mapping/FT_SO.txt>

       dgg: separated out FT_SO_map for caller changes. Update with:

         open(FTSO,"curl -s http://sequenceontology.org/resources/mapping/FT_SO.txt|");
         while(<FTSO>){
           chomp; ($ft,$so,$sid,$ftdef,$sodef)= split"\t";
           print "     '$ft' => '$so',\n" if($ft && $so && $ftdef);
         }

   get_relationship_type_by_parent_child
        Title   : get_relationship_type_by_parent_child
        Usage   : $type = $tm->get_relationship_type_by_parent_child($parent_sf, $child_sf);
        Usage   : $type = $tm->get_relationship_type_by_parent_child('mRNA', 'protein');
        Function: given two features where the parent contains the child,
                  will determine what the relationship between them in
        Example :
        Returns :
        Args    : parent SeqFeature, child SeqFeature OR
                  parent type string, child type string OR

       bioperl Seq::FeatureHolderI hierarchies are equivalent to unlabeled graphs (where parent
       nodes are the containers, and child nodes are the features being contained). For example,
       a feature of type mRNA can contain features of type exon.

       Some external representations (eg chadoxml or chaosxml) require that the edges in the
       feature relationship graph are labeled. For example, the type between mRNA and exon would
       be part_of. Although it stretches the bioperl notion of containment, we could have a CDS
       contained by an mRNA (for example, the Bio::SeqFeature::Tools::Unflattener module takes
       genbank records and makes these kind of links. The relationship here would be produced_by

       In chado speak, the child is the subject feature and the parent is the object feature