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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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Rename project #128

Open hammer opened 9 years ago

hammer commented 9 years ago

Not urgent but we have done the refactoring to make non-Ensembl data sources possible and we should acknowledge this fact in the name before publishing an application note.

iskandr commented 8 years ago

Unfortunately, pygenome is already taken.

Anyone (@armish, @tavinathanson, @timodonnell) have other ideas?

armish commented 8 years ago
tavinathanson commented 8 years ago

Looks like genompy is taken by a similar Ensembl library.

alec-djinn commented 8 years ago

pydjinn ;)

On Feb 5, 2016, at 23:04, Tavi Nathanson notifications@github.com wrote:

Looks like genompy is taken by a similar Ensembl library.

— Reply to this email directly or view it on GitHub https://github.com/hammerlab/pyensembl/issues/128#issuecomment-180587739.

iskandr commented 8 years ago

@tavinathanson @timodonnell @arahuja Opinions on calling the project pygenes and having subdirectories for ensembl, ucsc, and maybe other data sources like VectorBase? Every subdir would have a corresponding genome object like ensembl.EnsemblGenome and ucsc.RefSeqGenome, each of which inherit from the source-agnostic pygenes.Genome.

armish commented 8 years ago

@iskandr: I like that idea and also the new name: simple and to the point. If there is no immediate use case, I would say don't worry about resources like VectorBase but leave the door open for its implementation by other people.

tavinathanson commented 8 years ago

Digging the name pygenes!

hammer commented 7 years ago

Once we rename to Pygenes we may want to support CHESS as an alternate source of annotations.