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lib/Bio/FeatureIO/gff.pm  view on Meta::CPAN

  } else {

    if($type =~ /^\D+:\d+$/){
      #looks like an identifier
      $fta->identifier($type)
    } else {
      $fta->name($type);
    }
  }

  $feat->type($fta);

  my %attr = ();
  chomp $attribute_string;

  unless ( $attribute_string eq '.' ) {
    my @attributes = split ';', $attribute_string;
    foreach my $attribute (@attributes){
      my($key,$values) = split '=', $attribute;

      # remove leading and trailing quotes from values
      $values =~ s/^["']//;
      $values =~ s/["']$//; #' terminate the quote for emacs

      my @values = map{uri_unescape($_)} split ',', $values;

     #minor hack to allow for multiple instances of the same tag
      if ($attr{$key}) {
        my @tmparray = @{$attr{$key}};
        push @tmparray, @values;
        $attr{$key} = [@tmparray];
      } else {
        $attr{$key} = [@values];
      }
    }
  }

  #Handle Dbxref attributes
  if($attr{Dbxref} or $attr{dbxref}){
    foreach my $value (@{ $attr{Dbxref} }, @{ $attr{dbxref} }){
      my $a = Bio::Annotation::DBLink->new();
      my($db,$accession) = $value =~ /^(.+?):(.+)$/;

      if(!$db or !$accession){ #dbxref malformed
        $self->throw("Error in line:\n$feature_string\nDbxref value '$value' did not conform to GFF3 specification");
        next;
      }

      $a->database($db);
      $a->primary_id($accession);
      $feat->add_Annotation('Dbxref',$a);
    }
  }

  #Handle Ontology_term attributes
  if($attr{Ontology_term}){
    foreach my $id (@{ $attr{Ontology_term} }){
      my $a = Bio::Annotation::OntologyTerm->new();

      if($self->validate()){
        my $ont_name = Bio::Ontology::OntologyStore->guess_ontology($id);
        my $ont = Bio::Ontology::OntologyStore->get_ontology($ont_name);
        my($term) = $ont->find_terms(-identifier => $id);
        $a->term($term);
      } else {
        $a->identifier($id);
      }

      $feat->add_Annotation('Ontology_term',$a);
    }
  }

  #Handle Gap attributes
  if($attr{Gap}){
     for my $value (@{ $attr{Gap} }) {
       my $a = Bio::Annotation::SimpleValue->new();
       $a->value($value);
       $feat->add_Annotation('Gap',$a);
     }
  }

  #Handle Target attributes
  if($attr{Target}){
    my $target_collection = Bio::Annotation::Collection->new();

    foreach my $target_string (@{ $attr{Target} } ) {

      #only replace + for space if + has been used in place of it
      #that is, + could also mean plus strand, and we don't want
      #to accidentally remove it
 
      #presumably you can't use + for space and + for strand in the same string.      
      $target_string =~ s/\+/ /g unless $target_string =~ / /; 

      my ($t_id,$tstart,$tend,$strand,$extra) = split /\s+/, $target_string; 
      if (!$tend || $extra) { # too much or too little stuff in the string
        $self->throw("The value in the Target string, $target_string, does not conform to the GFF3 specification");
      }

      my $a = Bio::Annotation::Target->new(
           -target_id => $t_id,
           -start     => $tstart,
           -end       => $tend,
      );

      if ($strand && $strand eq '+') {
        $strand = 1;
      } elsif ($strand && $strand eq '-') {
        $strand = -1;
      } else {
        $strand = '';
      }

      $a->strand($strand) if $strand;
      $feat->add_Annotation('Target',$a); 
    }
  }

  #Handle ID attribute.  May only have one ID, throw error otherwise

  if($attr{ID}){