Bio::DB::Taxonomy flatfile
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Summary
Bio::DB::Taxonomy::flatfile - Use the NCBI taxonomy from local indexed flat files
Package variables
No package variables defined.
Included modules
Bio::Taxon
DB_File
File::Spec::Functions
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
newDescriptionCode
get_num_taxaDescriptionCode
get_taxonDescriptionCode
get_taxonidsDescriptionCode
get_Children_TaxidsDescriptionCode
ancestorDescriptionCode
each_DescendentDescriptionCode
_build_index
No description
Code
_db_connect
No description
Code
index_directoryDescriptionCode
Methods description
newcode    nextTop
 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
get_num_taxacodeprevnextTop
 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
get_taxoncodeprevnextTop
 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)
get_taxonidscodeprevnextTop
 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
get_Children_TaxidscodeprevnextTop
 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())
ancestorcodeprevnextTop
 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)
each_DescendentcodeprevnextTop
 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)
index_directorycodeprevnextTop
 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
newdescriptionprevnextTop
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 $self;
}
get_num_taxadescriptionprevnextTop
sub get_num_taxa {
    my ($self) = @_;
    if (not exists $self->{_num_taxa}) {
        my $num = 0;
        while ( my ($parent, undef) = each %{$self->{_parent2children}} ) {
           $num++;
        }
        $self->{_num_taxa} = $num;
    }
    return $self->{_num_taxa};
}
get_taxondescriptionprevnextTop
sub get_taxon {
    my ($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 $taxon; } *get_Taxonomy_Node =\& get_taxon;
}
get_taxonidsdescriptionprevnextTop
sub get_taxonids {
    my ($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, $ids); return wantarray() ? @ids : shift @ids; } *get_taxonid =\& get_taxonids;
}
get_Children_TaxidsdescriptionprevnextTop
sub get_Children_Taxids {
   my ($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;
}
ancestordescriptionprevnextTop
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;
}
each_DescendentdescriptionprevnextTop
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;
}
_build_indexdescriptionprevnextTop
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
}
_db_connectdescriptionprevnextTop
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;
}
index_directorydescriptionprevnextTop
sub index_directory {
    my $self = shift;
    return $self->{'index_directory'} = shift if @_;
    return $self->{'index_directory'};
}


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 list. 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
of the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
CONTRIBUTORSTop
Sendu Bala: bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::DB::Taxonomy interface implementationTop
Helper methods Top