Summary

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

Package variables

Included modules

Inherit

Bio::Root::Root

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.

Methods

Methods description

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

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

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

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

Methods code

sub new {

    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    my($typemap) =
	$self->_rearrange([qw(TYPEMAP
			     )],
                          @args);

    $typemap  && $self->typemap($typemap);
    return $self; # success - we hope!

}

sub typemap {

    my $self = shift;

    return $self->{'typemap'} = shift if @_;
    return $self->{'typemap'};

}

sub map_types {

   my ($self,@args) = @_;

   my($sf, $seq, $type_map) =
     $self->_rearrange([qw(FEATURE
                           SEQ
			   TYPE_MAP
                          )],
                          @args);
   if (!$sf && !$seq) {
       $self->throw("you need to pass in either -feature or -seq");
   }

   my @sfs = ($sf);
   if ($seq) {
       $seq->isa("Bio::SeqI") || $self->throw("$seq NOT A SeqI");
       @sfs = $seq->get_all_SeqFeatures;
   }
   $type_map = $type_map || $self->type_map;
   foreach my $sf (@sfs) {

       $sf->isa("Bio::SeqFeatureI") || $self->throw("$sf NOT A SeqFeatureI");
       $sf->isa("Bio::FeatureHolderI") || $self->throw("$sf NOT A FeatureHolderI");

       my $type = $sf->primary_tag;
       my $mtype = $type_map->{$type};
       if ($mtype) {
	   if (ref($mtype)) {
	       if (ref($mtype) eq 'CODE') {
		   $mtype = $mtype->($sf);
	       }
	       else {
		   $self->throw('must be scalar or CODE ref');
	       }
	   }
	   $sf->primary_tag($mtype);
       }
   }
   return;

}

sub map_types_to_SO {

   my ($self,@args) = @_;

   push(@args,
	(-type_map=>{

		     # this is the most generic form for RNAs;
		     # we always represent the processed form of
		     # the transcript
		     misc_RNA=>'processed_transcript',

		     misc_feature=>'located_sequence_feature',

		     # not sure about this one...
		     source=>'databank_entry',

		     LTR=>'LTR_retrotransposon',

		     rep_origin=>'origin_of_replication',

                     # this should really be subtyped...
                     variation=>'sequence_variant',

		     "5'UTR"=>'five_prime_UTR',
		     "3'UTR"=>'three_prime_UTR',
		     
		    }));
   return $self->map_types(@args);

}

General documentation

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
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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 _