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Summary

Bio::DB::Taxonomy::flatfile - Use the NCBI taxonomy from local indexed flat files

Package variables

Included modules

Inherit

Bio::DB::Taxonomy

Synopsis

  use Bio::DB::Taxonomy;

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

Description

This is an implementation of Bio::DB::Taxonomy which stores and accesses the
NCBI taxonomy using flat files stored locally on disk and indexed using the
DB_File module RECNO data structure for fast retrieval.
The required database files, nodes.dmp and names.dmp can be obtained from
ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::DB::Taxonomy::flatfile->new();
 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 to replace current indexes even if they exist

 Title   : get_num_taxa
 Usage   : my $num = $db->get_num_taxa();
 Function: Get the number of taxa stored in the database.
 Returns : A number
 Args    : None

 Title   : get_taxon
 Usage   : my $taxon = $db->get_taxon(-taxonid => $taxonid)
 Function: Get a Bio::Taxon object from the database.
 Returns : Bio::Taxon object
 Args    : just a single value which is the database id, OR named args:
           -taxonid => taxonomy id (to query by taxonid)
            OR
           -name    => string (to query by a taxonomy name: common name, 
                               scientific name, etc)

 Title   : get_taxonids
 Usage   : my @taxonids = $db->get_taxonids('Homo sapiens');
 Function: Searches for a taxonid (typically ncbi_taxon_id) based on a query
           string. Note that multiple taxonids can match to the same supplied
           name.
 Returns : array of integer ids in list context, one of these in scalar context
 Args    : string representing taxon's name

 Title   : get_Children_Taxids
 Usage   : my @childrenids = $db->get_Children_Taxids 
 Function: Get the ids of the children of a node in the taxonomy
 Returns : Array of Ids
 Args    : Bio::Taxon or a taxon_id
 Status  : deprecated (use each_Descendent())

 Title   : ancestor
 Usage   : my $ancestor_taxon = $db->ancestor($taxon)
 Function: Retrieve the full ancestor taxon of a supplied Taxon from the
           database. 
 Returns : Bio::Taxon
 Args    : Bio::Taxon (that was retrieved from this database)

 Title   : each_Descendent
 Usage   : my @taxa = $db->each_Descendent($taxon);
 Function: Get all the descendents of the supplied Taxon (but not their
           descendents, ie. not a recursive fetchall).
 Returns : Array of Bio::Taxon objects
 Args    : Bio::Taxon (that was retrieved from this database)

 Title   : index_directory
 Funtion : Get/set the location that index files are stored. (this module
           will index the supplied database)
 Usage   : $obj->index_directory($newval)
 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_num_taxa {

    my ($self) = @_;
    if (not exists $self->{_num_taxa}) {
        my $num = 0;
        while ( my ($parent, undef) = each %{$self->{_parent2children}} ) {
           $num++;
        }
        $self->{_num_taxa} = $num;
    }
    return $self->{_num_taxa};

}

sub get_taxon {

    my ($self) = shift;
    my ($taxonid, $name);
 
    if (@_ > 1) {
        ($taxonid, $name) = $self->_rearrange([qw(TAXONID NAME)],@_);
        if ($name) {
            ($taxonid, my @others) = $self->get_taxonids($name);
            $self->warn("There were multiple ids ($taxonid @others) matching '$name', using '$taxonid'") if @others > 0;
        }
    }
    else {  
        $taxonid = shift;
    }
    
    return unless $taxonid;
    
    $taxonid =~ /^\d+$/ || return;
    my $node = $self->{'_nodes'}->[$taxonid] || return;
    length($node) || return;
    my ($taxid, undef, $rank, $code, $divid, $gen_code, $mito) = split(SEPARATOR,$node);
    last unless defined $taxid;
    my ($taxon_names) = $self->{'_id2name'}->[$taxid];
    my ($sci_name, @common_names) = split(SEPARATOR, $taxon_names);
    
    my $taxon = Bio::Taxon->new(
                        -name         => $sci_name,
                        -common_names => [@common_names],
                        -ncbi_taxid   => $taxid, # since this is a real ncbi taxid, explicitly set it as one
                        -rank         => $rank,
                        -division     => $DIVISIONS[$divid]->[1],
                        -genetic_code => $gen_code,
                        -mito_genetic_code => $mito );
    # we can't use -dbh or the db_handle() method ourselves or we'll go
    # infinite on the merge attempt
    $taxon->{'db_handle'} = $self;
    
    $self->_handle_internal_id($taxon);
    
    return $taxon;
}

*get_Taxonomy_Node =\& get_taxon;

}

sub get_taxonids {

    my ($self, $query) = @_;
    my $ids = $self->{'_name2id'}->{lc($query)};
    unless ($ids) {
        if ($query =~ /_/) {
            # try again converting underscores to spaces
            $query =~ s/_/ /g;
            $ids = $self->{'_name2id'}->{lc($query)};
        }
        $ids || return;
    }
    my @ids = split(SEPARATOR, $ids);
    return wantarray() ? @ids : shift @ids;
}

*get_taxonid =\& get_taxonids;

}

sub get_Children_Taxids {

   my ($self, $node) = @_;
   $self->warn("get_Children_Taxids is deprecated, use each_Descendent instead");
   my $id;
   if( ref($node) ) {
       if( $node->can('object_id') ) {
           $id = $node->object_id;
       } elsif( $node->can('ncbi_taxid') ) {
           $id = $node->ncbi_taxid;
       } else { 
           $self->warn("Don't know how to extract a taxon id from the object of type ".ref($node)."\n");
           return;
       }
   } else { $id = $node }
   my @vals = $self->{'_parentbtree'}->get_dup($id);
   return @vals;

}

sub ancestor {

    my ($self, $taxon) = @_;
    $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon');
    $self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self;
    my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!");
    
    my $node = $self->{'_nodes'}->[$id];
    if (length($node)) {
        my (undef, $parent_id) = split(SEPARATOR,$node);
        $parent_id || return;
        $parent_id eq $id && return; # one of the roots
        return $self->get_taxon($parent_id);
    }
    return;

}

sub each_Descendent {

    my ($self, $taxon) = @_;
    $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon');
    $self->throw("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_handle eq $self;
    my $id = $taxon->id || $self->throw("The supplied Taxon is missing its id!");

    my @desc_ids = $self->{'_parentbtree'}->get_dup($id);
    my @descs;
    foreach my $desc_id (@desc_ids) {
        push(@descs, $self->get_taxon($desc_id) || next);
    }
    return @descs;

}

sub _build_index {

    my ($self, $nodesfile, $namesfile, $force) = @_;
    
    my $dir = $self->index_directory;
    my $nodeindex         = catfile($dir, $DEFAULT_NODE_INDEX);
    my $name2idindex      = catfile($dir, $DEFAULT_NAME2ID_INDEX);
    my $id2nameindex      = catfile($dir, $DEFAULT_ID2NAME_INDEX);
    my $parent2childindex = catfile($dir, $DEFAULT_PARENT_INDEX);
    $self->{'_nodes'}           = [];
    $self->{'_id2name'}         = [];
    $self->{'_name2id'}         = {};
    $self->{'_parent2children'} = {};
    
    if (! -e $nodeindex || $force) {
        my (%parent2children,@nodes);
        open(NODES,$nodesfile) || 
            $self->throw("Cannot open node file '$nodesfile' for reading");
        
        unlink $nodeindex;
        unlink $parent2childindex;
        my $nh = tie ( @nodes, 'DB_File', $nodeindex, O_RDWR|O_CREAT, 0644, $DB_RECNO) || 
            $self->throw("Cannot open file '$nodeindex': $!");
        my $btree = tie( %parent2children, 'DB_File', $parent2childindex, O_RDWR|O_CREAT, 0644, $DB_BTREE) || 
            $self->throw("Cannot tie to file '$parent2childindex': $!");
        
        while (<NODES>) {
            chomp;
            my ($taxid,$parent,$rank,$code,$divid,undef,$gen_code,undef,$mito) = split(/\t\|\t/,$_);
            # don't include the fake root node 'root' with id 1; we essentially have multiple roots here
            next if $taxid == 1;
            if ($parent == 1) {
                $parent = $taxid;
            }

            # keep this stringified
            $nodes[$taxid] = join(SEPARATOR, ($taxid,$parent,$rank,$code,$divid,$gen_code,$mito));
            $btree->put($parent,$taxid);
        }
        close(NODES);
        
        $nh = $btree = undef;
        untie @nodes ;
        untie %parent2children;
    }
    
    if ((! -e $name2idindex || -z $name2idindex) || (! -e $id2nameindex || -z $id2nameindex) || $force) { 
        open(NAMES,$namesfile) || 
            $self->throw("Cannot open names file '$namesfile' for reading");
        
        unlink $name2idindex;
        unlink $id2nameindex;
        my (@id2name,%name2id);
        my $idh = tie (@id2name, 'DB_File', $id2nameindex, O_RDWR|O_CREAT, 0644, $DB_RECNO) || 
            $self->throw("Cannot tie to file '$id2nameindex': $!");
        my $nameh = tie ( %name2id, 'DB_File', $name2idindex, O_RDWR|O_CREAT, 0644, $DB_HASH) || 
            $self->throw("Cannot tie to file '$name2idindex': $!");
        
        while (<NAMES>) {
            chomp; 
            my ($taxid, $name, $unique_name, $class) = split(/\t\|\t/,$_);
            # don't include the fake root node 'root' or 'all' with id 1
            next if $taxid == 1;

            $class =~ s/\s+\|\s*$//;
            my $lc_name = lc($name);
            my $orig_name = $name;
            
            # unique names aren't always in the correct column, sometimes they
            # are uniqued by adding bracketed rank names to the normal name;
            # store the uniqued version then fix the name for normal use
            if ($lc_name =~ /\(class\)$/) { # it seems that only rank of class is ever used in this situation
                $name2id{$lc_name} = $taxid;
                $name =~ s/\s+\(class\)$//;
                $lc_name = lc($name);
            }
            
            # handle normal names which aren't necessarily unique
            my $taxids = $name2id{$lc_name} || '';
            my %taxids = map { $_ => 1 } split(SEPARATOR, $taxids);
            unless (exists $taxids{$taxid}) {
                $taxids{$taxid} = 1;
                $name2id{$lc_name} = join(SEPARATOR, keys %taxids);
            }
            
            # store unique names in name2id
            if ($unique_name) {
                $name2id{lc($unique_name)} = $taxid;
            }
            
            # store all names in id2name array
            my $names = $id2name[$taxid] || '';
            my @names = split(SEPARATOR, $names);
            if ($class && $class eq 'scientific name') {
                # the scientific name should be the first name stored
                unshift(@names, $name);
                push(@names, $orig_name) if ($orig_name ne $name);
                push(@names, $unique_name) if $unique_name;
            }
            else {
                # all other ('common' in this simplification) names get added after
                push(@names, $name);
                push(@names, $orig_name) if ($orig_name ne $name);
                push(@names, $unique_name) if $unique_name;
            }
            $id2name[$taxid] = join(SEPARATOR, @names);
        }
        close(NAMES);
        
        $idh = $nameh = undef;
        untie( %name2id);
        untie( @id2name);
    }
}


# connect the internal db handle

}

sub _db_connect {

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

    my $dir = $self->index_directory;
    my $nodeindex         = catfile($dir, $DEFAULT_NODE_INDEX);
    my $name2idindex      = catfile($dir, $DEFAULT_NAME2ID_INDEX);
    my $id2nameindex      = catfile($dir, $DEFAULT_ID2NAME_INDEX);
    my $parent2childindex = catfile($dir, $DEFAULT_PARENT_INDEX);
    $self->{'_nodes'}           = [];
    $self->{'_id2name'}         = [];
    $self->{'_name2id'}         = {};
    $self->{'_parent2children'} = {};
    
    if( ! -e $nodeindex ||
        ! -e $name2idindex || 
        ! -e $id2nameindex ) {
        $self->warn("Index files have not been created");
        return 0;
    }
    tie ( @{$self->{'_nodes'}}, 'DB_File', $nodeindex, O_RDWR,undef, $DB_RECNO) 
        || $self->throw("$! $nodeindex");
    tie (@{$self->{'_id2name'}}, 'DB_File', $id2nameindex,O_RDWR, undef, 
        $DB_RECNO) || $self->throw("$! $id2nameindex");
    
    tie ( %{$self->{'_name2id'}}, 'DB_File', $name2idindex, O_RDWR,undef, 
        $DB_HASH) || $self->throw("$! $name2idindex");
    $self->{'_parentbtree'} = tie( %{$self->{'_parent2children'}},
                                   'DB_File', $parent2childindex, 
                                   O_RDWR, 0644, $DB_BTREE);

    $self->{'_initialized'} = 1;

}

sub index_directory {

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


1;

}

General documentation

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with code and data examples if at all possible.

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