Bio::Tools::Run::Ensembl(3pm)				User Contributed Perl Documentation			     Bio::Tools::Run::Ensembl(3pm)

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)

perl v5.12.3							    2011-06-18					     Bio::Tools::Run::Ensembl(3pm)