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Bio::DB::Taxonomy::entUser3Contributed Perl DocumeBio::DB::Taxonomy::entrez(3)

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

   Support
       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 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

perl v5.14.1			  2011-07-22	  Bio::DB::Taxonomy::entrez(3)
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