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Bio::DB::Taxonomy::flatfile.3pm

NAME

Bio::DB::Taxonomy::flatfile - An implementation of Bio::DB::Taxonomy which uses local flat files

SYNOPSIS

   use Bio::DB::Taxonomy;
 
   my $db = Bio::DB::Taxonomy->new(-source => 'flatfile'
                                  -nodesfile => $nodesfile,
                                  -namesfile => $namefile);
 
 

DESCRIPTION

This is an implementation which uses local flat files and the DB_File module RECNO data structures to manage a local copy of the NCBI Taxonomy database.

Required database files can be obtained from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

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-dot-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::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 replace current indexes even if they exist
 
 

Bio::DB::Taxonomy Interface implementation

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)
 
 

get_taxonids

  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_Taxids

  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())
 
 

ancestor

  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_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).
  Returns : Array of Bio::Taxon objects
  Args    : Bio::Taxon (that was retrieved from this database)
 
 

Helper methods

index_directory

  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)