Bio::SeqFeature::Tools TypeMapper
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Summary
Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature->primary_tag
Package variables
No package variables defined.
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
newDescriptionCode
typemapDescriptionCode
map_typesDescriptionCode
FT_SO_map
No description
Code
map_types_to_SODescriptionCode
get_relationship_type_by_parent_childDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : $unflattener = Bio::SeqFeature::Tools::TypeMapper->new();
 Function: constructor
 Example : 
 Returns : a new Bio::SeqFeature::Tools::TypeMapper
 Args    : see below
typemapcodeprevnextTop
 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_typescodeprevnextTop
 Title   : map_types
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 dgg: added -undefined => "region" option to produce all valid SO mappings.
map_types_to_SOcodeprevnextTop
 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_childcodeprevnextTop
 Title   : get_relationship_type_by_parent_child
 Usage   : $type = $tm->get_relationship_type_by_parent_child($parent_sf, $child_sf);
 Usage   : $type = $tm->get_relationship_type_by_parent_child('mRNA', 'protein');
 Function: given two features where the parent contains the child,
           will determine what the relationship between them in
 Example :
 Returns : 
 Args    : parent SeqFeature, child SeqFeature OR
           parent type string, child type string OR
bioperl Seq::FeatureHolderI hierarchies are equivalent to unlabeled
graphs (where parent nodes are the containers, and child nodes are the
features being contained). For example, a feature of type mRNA can
contain features of type exon.
Some external representations (eg chadoxml or chaosxml) require that
the edges in the feature relationship graph are labeled. For example,
the type between mRNA and exon would be part_of. Although it
stretches the bioperl notion of containment, we could have a CDS
contained by an mRNA (for example, the
Bio::SeqFeature::Tools::Unflattener module takes genbank records
and makes these kind of links. The relationship here would be
produced_by
In chado speak, the child is the subject feature and the parent is
the object feature
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

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

    $typemap  && $self->typemap($typemap);
    return $self; # success - we hope!
}
typemapdescriptionprevnextTop
sub typemap {
    my $self = shift;

    return $self->{'typemap'} = shift if @_;
    return $self->{'typemap'};
}
map_typesdescriptionprevnextTop
sub map_types {
   my ($self,@args) = @_;

   my($sf, $seq, $type_map, $undefmap) =
     $self->_rearrange([qw(FEATURE
                           SEQ
			   TYPE_MAP
			   UNDEFINED
                          )],
                          @args);
   if (!$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->typemap; # dgg: was 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 {
		   $self->throw('type_map values must be scalar or CODE ref. You said: '.$mtype.' for type: '.$type);
	       }
	   }
	   elsif ($undefmap && $mtype eq 'undefined') { # dgg
	      $mtype= $undefmap;
           }
	   $sf->primary_tag($mtype);
       }
   }
   return;
}
FT_SO_mapdescriptionprevnextTop
sub FT_SO_map {
  # $self= shift;
  # note : some of the ft_so mappings are commented out and overriden...
    return {
	"-" => ["located_sequence_feature", "so:0000110"],
	"-10_signal" => ["minus_10_signal", "so:0000175"],
	"-35_signal" => ["minus_35_signal", "so:0000176"],
	"3'utr" => ["three_prime_utr", "so:0000205"],
	"3'clip" => ["three_prime_clip", "so:0000557"],
	"5'utr" => ["five_prime_utr", "so:0000204"],
	"5'clip" => ["five_prime_clip", "so:0000555"],
	"caat_signal" => ["caat_signal", "so:0000172"],
	"cds" => ["cds", "so:0000316"],
	"c_region" => ["undefined", ""],
	"d-loop" => ["d_loop", "so:0000297"],
	"d_segment" => ["d_gene", "so:0000458"],
	"gc_signal" => ["gc_rich_region", "so:0000173"],
	"j_segment" => ["undefined", ""],
	"ltr" => ["long_terminal_repeat", "so:0000286"],
	"n_region" => ["undefined", ""],
	"rbs" => ["ribosome_entry_site", "so:0000139"],
	"sts" => ["sts", "so:0000331"],
	"s_region" => ["undefined", ""],
	"tata_signal" => ["tata_box", "so:0000174"],
	"v_region" => ["undefined", ""],
	"v_segment" => ["undefined", ""],
	"attenuator" => ["attenuator", "so:0000140"],
	"conflict" => ["undefined", ""],
	"enhancer" => ["enhancer", "so:0000165"],
	"exon" => ["exon", "so:0000147"],
	"gap" => ["gap", "so:0000730"],
	"gene" => ["gene", "so:0000704"],
	"idna" => ["idna", "so:0000723"],
	"intron" => ["intron", "so:0000188"],
	"mRNA" => ["mRNA", "so:0000234"],
	"mat_peptide" => ["mature_protein_region", "so:0000419"],
	"mature_peptide" => ["mature_protein_region", "so:0000419"],
	#"misc_RNA" => ["transcript", "so:0000673"],
	"misc_binding" => ["binding_site", "so:0000409"],
	"misc_difference" => ["sequence_difference", "so:0000413"],
	"misc_feature" => ["region", undef],
	"misc_recomb" => ["recombination_feature", "so:0000298"],
	"misc_signal" => ["regulatory_region", "so:0005836"],
	"misc_structure" => ["sequence_secondary_structure", "so:0000002"],
	"modified_base" => ["modified_base_site", "so:0000305"],
	"old_sequence" => ["undefined", ""],
	"operon" => ["operon", "so:0000178"],
	"oriT" => ["origin_of_transfer", "so:0000724"],
	"polya_signal" => ["polyA_signal_sequence", "so:0000551"],
	"polya_site" => ["polyA_site", "so:0000553"],
	"precursor_RNA" => ["primary_transcript", "so:0000185"],
	"prim_transcript" => ["primary_transcript", "so:0000185"],
	"primer_bind" => ["primer_binding_site", "so:0005850"],
	"promoter" => ["promoter", "so:0000167"],
	"protein_bind" => ["protein_binding_site", "so:0000410"],
	"rRNA" => ["rRNA", "so:0000252"],
	"repeat_region" => ["repeat_region", "so:0000657"],
	"repeat_unit" => ["repeat_unit", "so:0000726"],
	"satellite" => ["satellite_dna", "so:0000005"],
	"scRNA" => ["scRNA", "so:0000013"],
	"sig_peptide" => ["signal_peptide", "so:0000418"],
	"snRNA" => ["snRNA", "so:0000274"],
	"snoRNA" => ["snoRNA", "so:0000275"],
	#"source" => ["databank_entry", "so:2000061"],
	"stem_loop" => ["stem_loop", "so:0000313"],
	"tRNA" => ["tRNA", "so:0000253"],
	"terminator" => ["terminator", "so:0000141"],
	"transit_peptide" => ["transit_peptide", "so:0000725"],
	"unsure" => "undefined",
	"variation" => ["sequence_variant", "so:0000109"],

	# manually added 
	## has parent = pseudogene ; dgg
	"pseudomRNA" => ["pseudogenic_transcript", "so:0000516"],
	## from unflattener misc_rna ; dgg
	"pseudotranscript" => ["pseudogenic_transcript", "so:0000516"],
	"pseudoexon" => ["pseudogenic_exon", "so:0000507"],
	"pseudoCDS" => ["pseudogenic_exon", "so:0000507"],
	"pseudomisc_feature" => ["pseudogenic_region", "so:0000462"],
	"pseudointron" => ["pseudogenic_region", "so:0000462"],


	## "undefined" => "region",

	# this is the most generic form for rnas;
	# we always represent the processed form of
	# the transcript
	misc_RNA => ['mature_transcript',"so:0000233"],

	# not sure about this one...
	source=>['contig', "SO:0000149"],

	rep_origin=>['origin_of_replication',"SO:0000296"],

	Protein=>['polypeptide',"SO:0000104"],
    };
#  return {
     #"FT term" => "SO term",
     #"-" => "located_sequence_feature",
     #"-10_signal" => "minus_10_signal",
     #"-35_signal" => "minus_35_signal",
     #"3'UTR" => "three_prime_UTR",
     #"3'clip" => "three_prime_clip",
     #"5'UTR" => "five_prime_UTR",
     #"5'clip" => "five_prime_clip",
     #"CAAT_signal" => "CAAT_signal",
     #"CDS" => "CDS",
     #"C_region" => "undefined",
     #"D-loop" => "D_loop",
     #"D_segment" => "D_gene",
     #"GC_signal" => "GC_rich_region",
     #"J_segment" => "undefined",
     #"LTR" => "long_terminal_repeat",
     #"N_region" => "undefined",
     #"RBS" => "ribosome_entry_site",
     #"STS" => "STS",
     #"S_region" => "undefined",
     #"TATA_signal" => "TATA_box",
     #"V_region" => "undefined",
     #"V_segment" => "undefined",
     #"attenuator" => "attenuator",
     #"conflict" => "undefined",
     #"enhancer" => "enhancer",
     #"exon" => "exon",
     #"gap" => "gap",
     #"gene" => "gene",
     #"iDNA" => "iDNA",
     #"intron" => "intron",
     #"mRNA" => "mRNA",
     #"mat_peptide" => "mature_protein_region",
     #"mature_peptide" => "mature_protein_region",
##                     "misc_RNA" => "transcript",
     #"misc_binding" => "binding_site",
     #"misc_difference" => "sequence_difference",
     #"misc_feature" => "region",
     #"misc_recomb" => "recombination_feature",
     #"misc_signal" => "regulatory_region",
     #"misc_structure" => "sequence_secondary_structure",
     #"modified_base" => "modified_base_site",
     #"old_sequence" => "undefined",
     #"operon" => "operon",
     #"oriT" => "origin_of_transfer",
     #"polyA_signal" => "polyA_signal_sequence",
     #"polyA_site" => "polyA_site",
     #"precursor_RNA" => "primary_transcript",
     #"prim_transcript" => "primary_transcript",
     #"primer_bind" => "primer_binding_site",
     #"promoter" => "promoter",
     #"protein_bind" => "protein_binding_site",
     #"rRNA" => "rRNA",
     #"repeat_region" => "repeat_region",
     #"repeat_unit" => "repeat_unit",
     #"satellite" => "satellite_DNA",
     #"scRNA" => "scRNA",
     #"sig_peptide" => "signal_peptide",
     #"snRNA" => "snRNA",
     #"snoRNA" => "snoRNA",
##                     "source" => "databank_entry",
     #"stem_loop" => "stem_loop",
     #"tRNA" => "tRNA",
     #"terminator" => "terminator",
     #"transit_peptide" => "transit_peptide",
     #"unsure" => "undefined",
     #"variation" => "sequence_variant",

      #"pseudomRNA" => "pseudogenic_transcript", ## has parent = pseudogene ; dgg
      #"pseudotranscript" => "pseudogenic_transcript", ## from Unflattener misc_RNA ; dgg
      #"pseudoexon" => "pseudogenic_exon",
      #"pseudoCDS"  => "pseudogenic_exon",
      #"pseudomisc_feature" => "pseudogenic_region",
      #"pseudointron" => "pseudogenic_region",
      
      ### "undefined" => "region",

      ## this is the most generic form for RNAs;
      ## we always represent the processed form of
      ## the transcript
      #misc_RNA=>'processed_transcript',
      
      ## not sure about this one...
      #source=>'contig',
      
      #rep_origin=>'origin_of_replication',
      
      #Protein=>'protein',
      #};
}
map_types_to_SOdescriptionprevnextTop
sub map_types_to_SO {
   my ($self,@args) = @_;

   push(@args, (-type_map=> $self->FT_SO_map() ) );
   return $self->map_types(@args);
}
get_relationship_type_by_parent_childdescriptionprevnextTop
sub get_relationship_type_by_parent_child {
   my ($self,$parent,$child) = @_;
   $parent = ref($parent) ? $parent->primary_tag : $parent;
   $child = ref($child) ? $child->primary_tag : $child;

   my $type = 'part_of'; # default

   # TODO - do this with metadata, or infer via SO itself

   if (lc($child) eq 'protein') {
       $type = 'derives_from';
   }
   if (lc($child) eq 'polypeptide') {
       $type = 'derives_from';
   }
   return $type;
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris MungallTop
Email: cjm@fruitfly.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _