Bio::DB::Taxonomy::entrez.3pm

Langue: en

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

# Do not use this object directly, rather through the Bio::DB::Taxonomy # interface
   use Bio::DB::Taxonomy;
 
   my $db = Bio::DB::Taxonomy->new(-source => 'entrez');
 
   my $taxonid = $db->get_taxonid('Homo sapiens');
   my $node   = $db->get_Taxonomy_Node(-taxonid => $taxonid);
 
   my $gi = 71836523;
   my $node = $db->get_Taxonomy_Node(-gi => $gi, -db => 'protein');
   print $node->binomial, "\n";
   my ($species,$genus,$family) =  $node->classification;
   print "family is $family\n";
 
   # Can also go up 4 levels
   my $p = $node;  
   for ( 1..4 ) { 
     $p = $db->get_Taxonomy_Node(-taxonid => $p->parent_id);
   }
   print $p->rank, " ", ($p->classification)[0], "\n";
 
   # could then classify a set of BLAST hits based on their GI numbers
   # into taxonomic categories.
 
 

It is not currently possibly to query a node for its children so we cannot completely replace the advantage of the flatfile Bio::DB::Taxonomy::flatfile module.

DESCRIPTION

A driver for querying NCBI Entrez Taxonomy database.

FEEDBACK

Mailing Lists

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
 
 

Reporting Bugs

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:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

Sendu Bala: bix@sendu.me.uk

APPENDIX

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

new

  Title   : new
  Usage   : my $obj = Bio::DB::Taxonomy::entrez->new();
  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
 
 

get_taxon

  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)
             OR
            To retrieve a taxonomy node for a GI number provide the -gi option
            with the gi number and -db with either 'nucleotide' or 'protein' to
            define the db.
             AND optionally,
            -full    => 1 (to force retrieval of full information - sometimes
                           minimal information about your taxon may have been
                           cached, which is normally used to save database
                           accesses)
 
 

get_taxonids

  Title   : get_taxonids
  Usage   : my $taxonid = $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
 
 

ancestor

  Title   : ancestor
  Usage   : my $ancestor_taxon = $db->ancestor($taxon)
  Function: Retrieve the ancestor taxon of a supplied Taxon from the database.
 
            Note that unless the ancestor has previously been directly
            requested with get_taxon(), the returned Taxon object will only have
            a minimal amount of information.
 
  Returns : Bio::Taxon
  Args    : Bio::Taxon (that was retrieved from this database)
 
 

each_Descendent

  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).
 
            Note that this implementation is unable to return a taxon that
            hasn't previously been directly fetched with get_taxon(), or wasn't
            an ancestor of such a fetch.
 
  Returns : Array of Bio::Taxon objects
  Args    : Bio::Taxon (that was retrieved from this database)
 
 

Some Get/Setter methods

entrez_url

  Title   : entrez_url
  Usage   : $obj->entrez_url($newval)
  Function: Get/set entrez URL
  Returns : value of entrez url (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

entrez_params

  Title   : entrez_params
  Usage   : $obj->entrez_params($newval)
  Function: Get/set entrez params
  Returns : value of entrez_params (a hashref)
  Args    : on set, new value Hashref
 
 

Bio::DB::WebBase methods

proxy_string

  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'
 
 

proxy

  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)
 
 

authentication

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