Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::DB::Taxonomy::sqlite - SQLite-based implementation of Bio::DB::Taxonomy::flatfile


         use Bio::DB::Taxonomy;

         my $db = Bio::DB::Taxonomy->new(-source    => 'sqlite',
                                         -db        => 'mytax.db'  # default 'taxonomy.sqlite'
                                         -nodesfile => 'nodes.dmp',
                                         -namesfile => 'names.dmp');


       This is an implementation of Bio::DB::Taxonomy which stores and accesses the NCBI taxonomy
       using a simple SQLite3 database stored locally on disk.

       With this implementation, one can do the same basic searches as with the 'flatfile'
       database.  A test lookup of 1000 NCBI TaxIDs with full lineage information took about 2
       seconds on my older MacBook Pro laptop with an on-disk implementation.

       A few key differences:

       ·   You can use typical SQL syntax to run a query search; for instance, if you want you
           can run:

              @ids = sort $db->get_taxonids('Chloroflexi%');

       ·   In-memory database is allowed

             my $db = Bio::DB::Taxonomy->new(-source    => 'sqlite',
                                             -db        => ':memory:',
                                             -nodesfile => 'nodes.dmp',
                                             -namesfile => 'names.dmp');

       The required database files, nodes.dmp and names.dmp can be obtained from


       ·   Small optimizations, such as optimizing name lookups

       ·   Possibly use recursive CTE <> to do lineage

       ·   Clean up SQL (still kind of a mess right now)

       ·   Check compat. with other NCBI-specific Bio::DB::Taxonomy implementations

       ·   Plan out feasibility of allowing other backends (Neo4J, other DBI, etc)

       ·   Optionally calculate left/right ID values for TaxID nodes

       Beyond completing the implementation and optimization, this will likely be rolled into a
       more flexible backend at some future point.


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       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.
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       Please direct usage questions or support issues to the mailing list:

       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.

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       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:

AUTHOR - Chris Fields

       Email cjfields-at-cpan-dot-org


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

        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

   Bio::DB::Taxonomy interface implementation
        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

        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)
                  -name    => string (to query by a taxonomy name: common name,
                                      scientific name, etc)

        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
        Returns : array of integer ids in list context, one of these in scalar context
        Args    : string representing taxon's name

        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())

        Title   : ancestor
        Usage   : my $ancestor_taxon = $db->ancestor($taxon)
        Function: Retrieve the full ancestor taxon of a supplied Taxon from the
        Returns : Bio::Taxon
        Args    : Bio::Taxon (that was retrieved from this database)

        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
        Title   : index_directory
        Function : 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)
        Note    : kept for backwards compatibility with older DB_File implementation

        Title   : db_name
        Function : Get/set the name of the SQLite3 database where data is stored
        Usage   : $obj->db_name($newval)
        Returns : value of db_name (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

        Title   : cache_size
        Function : Get/set the cachesize used for loading the SQLite3 database
        Usage   : $obj->cache_size($newval)
        Returns : value of cache_size (a scalar)
        Args    : on set, new value (a scalar or undef, optional)
        Note    : we do no checking on whether this value is an integer (SQLite does this for use)