NAME

       Bio::Tools::Run::Ensembl - A simplified front-end for setting up the registry
                                  for, and then using an Ensembl database with the
                                  Ensembl Perl API.

SYNOPSIS

         use Bio::Tools::Run::Ensembl;

         # get a Bio::EnsEMBL::Gene for agene of interest
         my $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
                                                               -name => 'BRCA2');

DESCRIPTION

       This is a simple way of accessing the Ensembl database to retrieve gene information.
       Rather than learn the whole Ensembl Perl API, you only need to install it (that is, check
       it out from CVS: http://www.ensembl.org/info/docs/api/api_installation.html - ignore the
       information about BioPerl version) and then you can get information about a gene using
       get_gene_by_name().

       For gene retrieval it is especially useful compared to direct Ensembl Perl API usage since
       it can use information from alternate data sources (orthologues, Swissprot, Entrez) to get
       your gene.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

       Email bix@sendu.me.uk

APPENDIX

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

   registry_setup
        Title   : registry_setup
        Usage   : Bio::Tools::Run::Ensembl->registry_setup(-host => $host,
                                                           -user => $user);
                  if (Bio::Tools::Run::Ensembl->registry_setup) {...}
        Function: Configure the ensembl registy to use a certain database.
                  The database must be an Ensembl database compatible with the
                  Ensembl Perl API, and you must have that API installed for this
                  method to return true. Defaults to anonymous access to
                  ensembldb.ensembl.org
                  Or just ask if the registry is setup and the database ready to use.
        Returns : boolean (true if Registry loaded and ready to use)
        Args    : -host    => host name (defaults to 'ensembldb.ensembl.org')
                  -user    => username (defaults to 'anonymous')
                  -pass    => password (no default)
                  -port    => port (defaults to 3306)
                  -db_version => version of ensembl database to use, if different from
                                 your installed Ensembl modules
                  -verbose => boolean (1 to print messages during database connection)
                  -no_database => boolean (1 to disable database access, causing this
                                  method to always return false)

   get_adaptor
        Title   : get_adaptor
        Usage   : my $adaptor = Bio::Tools::Run::Ensembl->get_adaptor($species, $type);
        Function: Get a species-specific 'core' database adaptor, optionally of a
                  certain type.
        Returns : Bio::EnsEMBL::DBSQL::DBAdaptor, OR if a certain type requested, a
                  Bio::EnsEMBL::DBSQL::${type}Adaptor
        Args    : Bio::Species or string (species name) (REQUIRED), AND optionally
                  string (the type of adaptor, eg. 'Gene' or 'Slice').

   get_gene_by_name
        Title   : get_gene_by_name
        Usage   : my $gene = Bio::Tools::Run::Ensembl->get_gene_by_name();
        Function: Get a gene given species and a gene name. If multiple genes match
                  this combination, tries to pick the 'best' match.
        Returns : Bio::EnsEMBL::Gene
        Args    : -species => Bio::Species or string (species name), REQUIRED
                  -name => string: gene name, REQUIRED

                  If searching for the supplied gene name in the supplied species
                  results in no genes, or more than one, you can choose what else is
                  attempted in order to find just one gene:

                  -use_orthologues   => Bio::Species or string (species name), or array
                                        ref of such things: see if any of these
                                        supplied species have (unambiguously) a gene
                                        with the supplied gene name and if a
                                        (one-to-one) orthologue of that gene in that
                                        species is present in the main desired species
                                        supplied to -species, returns that orthologous
                                        gene. (default: none, do not use orthologues)
                  -use_swiss_lookup  => boolean: queries swissprot at expasy and if a
                                        suitable match is found, queries ensembl with
                                        the swissprot id. (default: 0, do not use
                                        swiss)
                  -use_entrez_lookup => boolean: queries entrez at the NCBI server if
                                        (only) a single gene could not be found by any
                                        other method, then query ensembl with the
                                        entrez gene id. (default: 0, do not use NCBI)

                  (Attempts proceed in this order and return as soon as one method is
                  successful.)

                  -strict => boolean: return undef with no warnings if more than one,
                             or zero genes were found. (default: 0, warnings are issued
                             and if many genes were found, one of them is returned)