Bio::T...nsembl(3pm)

💖 Bio::Tools::Run::Ensembl 💖

okay bestie, gather round, because this is the Perl module Bio::Tools::Run::Ensembl, and she is exactly what her name says: a simplified front-end for setting up the registry for, and then using an Ensembl database with the Ensembl Perl API. no cap. 🧬✨

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🌸 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');

(and yes, that comment really does say agene. we respect the original. 🫶)

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✨ DESCRIPTION ✨

So here's the vibe: this is a simple way of accessing the Ensembl database to retrieve gene information. Instead of learning the whole entire Ensembl Perl API (which, respectfully, is a lot), you literally only need to install it — meaning check it out from CVS, and the docs for that live at http://www.ensembl.org/info/docs/api/api_installation.html (just ignore the information about BioPerl version, ok? not relevant, we don't care 💅) — and then boom, you can get information about a gene using get_gene_by_name().

And for gene retrieval it is especially useful compared to direct Ensembl Perl API usage, because it can use information from alternate data sources — orthologues, Swissprot, Entrez — to get your gene. she's resourceful. main character energy fr fr. 👑

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🎀 FEEDBACK 🎀

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. So like, send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. genuinely!! 🥹

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. Because so many experienced and reponsive experts will be able look at the problem and quickly address it. (the original says "reponsive", and honestly? iconic typo, we keep it 💀)

Please include a thorough description of the problem with code and data examples if at all possible. the more tea you spill, the faster someone can help.

🐛 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/

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👑 AUTHOR - Sendu Bala

Email bix@sendu.me.uk

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📖 APPENDIX 📖

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

🔧 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. (yes, "registy". we said what we said. 🍓) 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 — plot twist — just ask if the registry is setup and the database ready to use. vibe check, basically. ✨

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)

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and that's the whole page, bestie!! 🦋 this was Bio::T...nsembl(3pm) from the User Contributed Perl Documentation, running on perl v5.36.0, dated 2023-01-22. slay, go get your genes. 💖🌈⭐