entrez documentation.

Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver

No package variables defined.

# Do not use this object directly, rather through the Bio::DB::Taxonomy
# interface

  use Bio::DB::Taxonomy;

  my $db = new Bio::DB::Taxonomy(-source => 'entrez');

  my $taxaid = $db->get_taxaid('Homo sapiens');

A driver for querying NCBI Entrez Taxonomy database.

sub _initialize {

  my($self) = shift;
  if( ! $XMLTWIG ) {
      $self->throw("Need to have installed XML::Twig");
  }

  $self->SUPER::_initialize(@_);

  my ($location,$params) = $self->_rearrange([qw(LOCATION PARAMS)],@_);

  $self->entrez_url($location || $EntrezLocation );
  if( $params ) {
      if( ref($params) !~ /HASH/i ) {
	  $self->warn("Must have provided a valid HASHref for -params");
	  $params =\% EntrezParams;
      }
  } else {
      $params =\% EntrezParams;
  }
  $self->entrez_params($params);
  $self->entrez_url($location || $EntrezLocation );

}

sub get_Taxonomy_Node {

   my ($self) = shift;
   my %p = $self->entrez_params;
   my $taxonid;
   if( @_ > 1 ) {
       my %params = @_;
       if( $params{'-taxonid'} ) {
	   $taxonid = $params{'-taxonid'};
       } elsif( $params{'-name'} ) {
	   my @taxaids = $self->get_taxonid($params{'-name'});
	   if( @taxaids > 1 ) { 
	       $self->warn("Got > 1 taxid for ".$params{'-name'}. " only using the first one");
	       $taxonid = shift @taxaids;
	   }
       } else { 
	   $self->warn("Need to have provided either a -taxonid or -name value to get_Taxonomy_Node");
       } 
   } else { 
       $taxonid= shift;
   }
   $p{'id'}      = $taxonid;

   my $params = join($UrlParamSeparatorValue, map { "$_=".$p{$_} } keys %p);
   my $url = sprintf("%s%s?%s",$self->entrez_url,$EntrezSummary,$params);
   $self->debug("url is $url\n")  if( $self->verbose > 0);
   my $response;
   eval {
       $response = $self->get($url);
   };
   if( $@ ) {
       $self->warn("Can't query website: $@");
       return;
   }
   my $twig = new XML::Twig;
   $self->debug( "resp is $response\n") if( $self->verbose > 0);
   $twig->parse($response);
   my $root = $twig->root;
   my $list = $root->first_child('DocSum');
   if( ! $list ) { 
       $self->warn("Could not find any value for $taxonid");
       return undef;
   }
   my ($id) = map { $_->text } $list->children('Id');

   my (%item) = map {  $_->{'att'}->{'Name'} => $_->text } $list->children('Item');

   if( $item{'RANK'} eq 'species') {
       my $node = new Bio::Species(-ncbi_taxid     => $id,
				   -common_name    => $item{'CommonName'},
				   -division       => $item{'Division'});
       my ($genus,$species,$subspecies) = split(' ',$item{'ScientificName'},3);
       $node->genus($species);
       $node->species($species);
       return $node;
   } else {
       $self->warn(sprintf("can't create a species object for %s (%s) because it isn't a species but is a '%s' instead",$item{'ScientificName'},$item{'CommonName'}, $item{'RANK'}));
   }\%
   item;

}

sub get_taxonid {

   my ($self,$query) = @_;
   my %p = $self->entrez_params;
   $query        =~ s/\s/\+/g;
   $p{'term'}      = $query;
   my $params = join($UrlParamSeparatorValue, map { "$_=".$p{$_} } keys %p);
   my $url = sprintf("%s%s?%s",$self->entrez_url,$EntrezGet,$params);
   my $response;
   eval {
       $response = $self->get($url);
   };
   if( $@ ) {
       $self->warn("Can't query website: $@");
       return;
   }
   $self->debug( "response is $response\n") if( $self->verbose > 0);

   my $twig = new XML::Twig;
   $twig->parse($response);
   my $root = $twig->root;
   my $list = $root->first_child('IdList');
   my @data = map { $_->text } $list->children('Id');
   ( wantarray ) ? @data : shift @data;

}

sub entrez_url {

    my $self = shift;

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

}

sub entrez_params {

    my $self = shift;
    my $f;
    if( @_ ) {
	$f = $self->{'_entrez_params'} = shift;
    } else {
	$f = $self->{'_entrez_params'};
    }
    return %$f;

}

General documentation

User feedback is an integral part of the evolution of this and other
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Email jason-at-bioperl.org

Additional contributors names and emails here

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

 Title   : new
 Usage   : my $obj = new Bio::DB::Taxonomy::entrez();
 Function: Builds a new Bio::DB::Taxonomy::entrez object
 Returns : an instance of Bio::DB::Taxonomy::entrez
 Args    : -location => URL to Entrez (if you want to override the default)
           -params   => Hashref of URL params if you want to override the
                        default

 Title   : proxy_string
 Usage   : my $proxy_string = $self->proxy_string($protocol)
 Function: Get the proxy string (plus user/pass )
 Returns : string
 Args    : protocol ('http' or 'ftp'), default 'http'

 Title   : proxy
 Usage   : $httpproxy = $db->proxy('http')  or
           $db->proxy(['http','ftp'], 'http://myproxy' )
 Function: Get/Set a proxy for use of proxy
 Returns : a string indicating the proxy
 Args    : $protocol : an array ref of the protocol(s) to set/get
           $proxyurl : url of the proxy to use for the specified protocol
           $username : username (if proxy requires authentication)
           $password : password (if proxy requires authentication)

 Title   : authentication
 Usage   : $db->authentication($user,$pass)
 Function: Get/Set authentication credentials
 Returns : Array of user/pass
 Args    : Array or user/pass

_initialize	No description	Code
get_Taxonomy_Node	Description	Code
get_taxonid	Description	Code
entrez_url	Description	Code
entrez_params	Description	Code