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

    my ($self) = $class->SUPER::new(@args);	
    $self->_initialize(@args);
    return $self;

  } else {

	my %param = @args;

	@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
	my $format = $param{'-format'} ||
      $class->_guess_format( $param{-file} || $ARGV[0] );
	
	if( ! $format ) {
      if ($param{-file}) {
        $format = $class->_guess_format($param{-file});
      } elsif ($param{-fh}) {
        $format = $class->_guess_format(undef);
      }
	}
	$format = "\L$format";	# normalize capitalization to lower case
	return unless( $class->_load_format_module($format) );
	return "Bio::FeatureIO::$format"->new(@args);

  }
}

=head2 newFh

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

 Args    : newvalue (optional)


=cut

sub _filehandle {
    my ($self,@args) = @_;
    return $self->_fh(@args);
}

=head2 _guess_format

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function: guess format based on file suffix
 Example :
 Returns : guessed format of filename (lower case)
 Args    :
 Notes   : See "SUPPORTED FORMATS"

=cut

sub _guess_format {
   my $class = shift;
   return unless $_ = shift;
   return 'gff'     if /\.gff3?$/i;
   return 'gff'     if /\.gtf$/i;
   return 'bed'     if /\.bed$/i;
   return 'ptt'     if /\.ptt$/i;

   return 'gff'; #the default
}

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

      $feat->add_Annotation('Dbxref',$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);
    }
  }