table of contents
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)
2023-01-22 | perl v5.36.0 |