NAME

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

SYNOPSIS

         use Bio::DB::Taxonomy;

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

DESCRIPTION

       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
       ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

TODO

       ·   Small optimizations, such as optimizing name lookups

       ·   Possibly use recursive CTE <http://www.sqlite.org/lang_with.html> to do lineage
           lookups

       ·   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.

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:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Chris Fields

       Email cjfields-at-cpan-dot-org

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 to replace current indexes even if they exist

   Bio::DB::Taxonomy interface implementation
   get_num_taxa
        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

   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
        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

   db_name
        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)

   cache_size
        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)