Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature->primary_tag 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); 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.

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/ Email: cjm@fruitfly.org 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!!!