+3
posted by Alejandro Sifrim, updated 3 years ago , 2
A script that automatically installs and/or updates a local ensembl mirror would certainly be handy.
It would check if the database config file is non-standard and download the sources from the ensembl ftp, create the new databases and import the data.
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+3
posted by Francesco Strozzi, 3 years ago , 0
The FuncGen database should be added to the list of Ensembl databases supported by the Ruby API
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+3
posted by Jan Aerts, 3 years ago , 0
The compara database should be added to the API.
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+1
ANSWERED
posted by Jan Aerts, updated 3 years ago , 0
A manuscript describing the Ruby Ensembl API has been published in Bioinformatics in 2011. Please use the following reference:

Strozzi F & Aerts J. A Ruby API to query the Ensembl databas for genomic features. Bioinformatics 27(7):1013-1014 (2011) [doi:10.1093/bioinformatics/btr050]
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+1
posted by Francesco Strozzi, 3 years ago , 0
Release 62 has changed a bit the way variation consequences are named. A check is needed to upgrade the code and the tests.

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+1
ANSWERED
posted by Jan Aerts, updated 3 years ago , 0
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Official answer
This Ruby API should have at least the same functionality as the Perl API for the Ensembl database, at least for what the core and variation databases are concerned (getting features, recalculations positions between coordinate systems, handling slices, ...)

There are some additional features in this API that are not available in the Perl version. For example, you do not need to change to a new API whenever there is a new release of the database; the Ruby API takes care of this automatically. In addition, you do not have to create separate Adaptor objects before you can access single objects. With this API, it is for example also possible to intersect and union Slice objects.
Official reply posted by Jan Aerts , 3 years ago
0
posted by Jan Aerts, updated 3 years ago , 1

(asked by Nick - nbshannon - on the github issues page)


I can get a slice and return genes contained by that slice with slice.genes however now this only returns genes fully contained by the slice, rather than any which overlap.

e.g.
Slice.fetch_by_region('chromosome','11',532242,537287,-1).genes.map{|gene| gene.display_name}
gives HRAS
however 
Slice.fetch_by_region('chromosome','11',532243,537287,-1).genes.map{|gene| gene.display_name}
gives nothing, since the slice is now 1 bp into the gene.

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0
posted by Ben Woodcroft, updated 3 years ago , 2
Currently, if Ensembl::Core::DBConnection.connect fails to connect to the database, then an ActiveRecord::ConnectionAdapters::MysqlAdapter is still returned.

Thanks,
ben
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0
posted by Ben Woodcroft, 3 years ago , 0
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