Summary

Bio::DB::Taxonomy::flatfile - An implementation of Bio::DB::Taxonomy
which uses local flat files

Package variables

Included modules

Inherit

Bio::DB::Taxonomy

Synopsis

  use Bio::DB::Taxonomy;

  my $db = new Bio::DB::Taxonomy(-source => 'flatfile'
                                 -nodesfile => $nodesfile,
                                 -namesfile => $namefile);

Description

This is an implementation which uses local flat files and the DB_File
module RECNO data structures to manage a local copy of the NCBI
Taxonomy database.
File can be obtained from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::DB::Taxonomy::flatfile();
 Function: Builds a new Bio::DB::Taxonomy::flatfile object 
 Returns : an instance of Bio::DB::Taxonomy::flatfile
 Args    : -directory => name of directory where index files should be created
           -nodesfile => name of file containing nodes (nodes.dmp from NCBI)
           -namesfile => name of the file containing names(names.dmp from NCBI)
           -force     => 1 replace current indexes even if they exist

 Title   : get_Taxonomy_Node
 Usage   : my $species = $db->get_Taxonomy_Node(-taxonid => $taxaid)
 Function: Get a Bio::Taxonomy::Taxon object for a taxonid
 Returns : Bio::Taxonomy::Taxon object
 Args    : -taxonid => taxonomy id (to query by taxonid)
            OR
           -name   => string (to query by a taxonomy name: common name, 
                              species, genus, etc)

 Title   : get_taxonid
 Usage   : my $taxonid = $db->get_taxonid('Homo sapiens');
 Function: Searches for a taxonid (typically ncbi_taxon_id) 
           based on a query string 
 Returns : Integer ID
 Args    : String representing species/node name

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

Methods code

sub new {

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

  my $self = $class->SUPER::new(@args);
  my ($dir,$nodesfile,$namesfile,$force) = $self->_rearrange([qw(DIRECTORY
								 NODESFILE
								 NAMESFILE
								 FORCE)],
							     @args);
  
  $self->index_directory($dir || $DEFAULT_INDEX_DIR);
  if ( $nodesfile ) {
      $self->_build_index($nodesfile,$namesfile,$force);
  }

  $self->_db_connect;
  return $self;

}

sub get_Taxonomy_Node {

   my ($self) = shift;
   my (%item,$taxonid,$name);

   if( @_ > 1 ) {
       ($taxonid,$name) = $self->_rearrange([qw(TAXONID
						NAME)],@_);
       if( $name ) {
	   ($taxonid) = $self->get_taxonid($name);
       }
   } else {  
       $taxonid = shift;
   }
   my $orig_taxonid = $taxonid;
   my (@fields,$node,$taxonnode);
   my $first = 1;
   while( defined ($node = $self->{'_nodes'}->[$taxonid]) ) {
       my ($taxid,$parent,$rank,$code,$divid) = split(SEPARATOR,$node);
       my ($taxon_name) = $self->{'_id2name'}->[$taxid];
       push @fields, $taxon_name if ($rank && $rank ne 'no rank') ;
       if( $first ) {	   
	   $taxonnode = new Bio::Taxonomy::Node(-dbh       => $self,
						-name      => $taxon_name,
						-object_id => $taxid,
						-parent_id => $parent,
						-rank      => $rank,
						-division  => $DIVISIONS[$divid]->[0]);
	   $first = 0;
       }

       last if $parent == 1 || ! $parent || ! $taxid;
       $taxonid = $parent;
   }

   my $speciesnode = new Bio::Species(-ncbi_taxid     => $orig_taxonid,
#				      -common_name    => $item{'CommonName'},
#				      -division       => $item{'Division'});
				      -classification => [@fields],
				      );
   return $taxonnode;

}

sub get_taxonid {

    my ($self,$query) = @_;
    my $id = $self->{'_name2id'}->{lc($query)};
    if( $id ) { 
	my ($taxid,$name,$fullname) = split(/:/,$id);
	return $taxid;
    }
    return 0;

}

sub _build_index {

    my ($self,$nodesfile,$namesfile,$force) = @_;
    
    my ($dir) = ($self->index_directory);
    my $nodeindex = "$dir/$DEFAULT_NODE_INDEX";
    my $name2idindex = "$dir/$DEFAULT_NAME2ID_INDEX";
    my $id2nameindex = "$dir/$DEFAULT_ID2NAME_INDEX";
    $self->{'_nodes'}    = [];
    $self->{'_id2name'} = [];
    $self->{'_name2id'} = {};
        
    if( ! -e $nodeindex || $force ) {
	open(NODES,$nodesfile) || 
	    $self->throw("Cannot open node file '$nodesfile' for reading");
	
	unlink $nodeindex;
	tie ( @{$self->{'_nodes'}}, 'DB_File', $nodeindex, O_RDWR|O_CREAT, 
	      0644, $DB_RECNO) || 
		  $self->throw("Cannot open file '$nodeindex': $!");	
	while(<NODES>) {
	    chomp;
	    my ($taxid,$parent,$rank,$code,$divid) = split(/\t\|\t/,$_);
	    # keep this stringified
	    $self->{'_nodes'}->[$taxid] = join(SEPARATOR, 
					       ($taxid,$parent,$rank,
						$code,$divid));
	}
	close(NODES);
	undef $self->{'_nodes'};
	untie( @{$self->{'_nodes'}} );
    }
    if( ! -e $name2idindex || ! -e $id2nameindex || $force ) { 
	open(NAMES,$namesfile) || 
	    $self->throw("Cannot open names file '$namesfile' for reading");

	unlink $name2idindex;
	unlink $id2nameindex;

	tie (@{$self->{'_id2name'}}, 'DB_File', $id2nameindex, 
	     O_RDWR|O_CREAT, 0644, $DB_RECNO) || 
		 $self->throw("Cannot open file '$id2nameindex': $!");
	
	tie ( %{$self->{'_name2id'}}, 'DB_File', $name2idindex, O_RDWR|O_CREAT, 
	      0644, $DB_HASH) || 
		  $self->throw("Cannot open file '$name2idindex': $!");
	
	while(<NAMES>) {
	    chomp;	    
	    my ($taxid,$name,$uniquename,$class) = split(/\t\|\t/,$_);
	    $class =~ s/\s+\|\s*$//;
	    $uniquename = $name unless $uniquename;
	    my $idx = lc($name);
	    $self->{'_name2id'}->{$idx} = join(SEPARATOR,
					       ($taxid, $name,$uniquename,
						$class));
	    if( $class && $class eq 'scientific name' ) {
		# only store the id2name lookup when it is the "proper" name
		$self->{'_id2name'}->[$taxid] = $uniquename;
	    }
	}
	close(NAMES);
	undef $self->{'_id2name'};
	undef $self->{'_name2id'};
	untie( %{$self->{'_name2id'}} );
	untie( @{$self->{'_id2name'}} );
    }

}

sub _db_connect {

    my $self = shift;
    return if $self->{'_initialized'};

#    undef $self->{'_nodes'};
#    undef $self->{'_id2name'};
#    undef $self->{'_name2id'};
#    untie( %{$self->{'_name2id'}} );
#    untie( @{$self->{'_id2name'}} );
#    untie( @{$self->{'_nodes'}} );
    
    $self->{'_nodes'}   = [];
    $self->{'_id2name'} = [];
    $self->{'_name2id'} = {};

    my ($dir) = ($self->index_directory);
    my $nodeindex = "$dir/$DEFAULT_NODE_INDEX";
    my $name2idindex = "$dir/$DEFAULT_NAME2ID_INDEX";
    my $id2nameindex = "$dir/$DEFAULT_ID2NAME_INDEX";
    if( ! -e $nodeindex ||
	! -e $name2idindex || 
	! -e $id2nameindex ) {
	$self->warn("Index files have not been created");
	return 0;
    }
    tie ( @{$self->{'_nodes'}}, 'DB_File', 
	  $nodeindex, O_RDONLY,0644, $DB_RECNO) 
	|| $self->throw("$! $nodeindex");
    tie (@{$self->{'_id2name'}}, 'DB_File', $id2nameindex,O_RDONLY, 0644, 
	 $DB_RECNO) || $self->throw("$! $id2nameindex");
    
    tie ( %{$self->{'_name2id'}}, 'DB_File', $name2idindex, O_RDONLY,0644, 
	  $DB_HASH) || $self->throw("$! $name2idindex");
    $self->{'_initialized'}  = 1;

}

sub index_directory {

    my $self = shift;

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

}

General documentation

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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _