Reference

Bio::DB::Taxonomy::sqlite(3pm)

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

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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)

History