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biocommons / uta

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
Apache License 2.0
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Python3 updates #219

Closed zackzwiesler0 closed 5 years ago

zackzwiesler0 commented 5 years ago

I want to run an automated script in a python3 environment. This PR should just do two things:

1) Makes the minimum amount of python3 upgrades to get my script to run. 2) Replaces the pg-dump-schema-rename regex replacement with a simple one, because I think all that needs to happen is the replacement of the schema name, and this was failing as is for my enviroment.

reece commented 5 years ago

@zackzwiesler0 Thanks for the PR. I'm merging even though I haven't tested them. (That's def not my usual practice!)

I will make some significant changes to UTA in the next few months, pending some expected funding. If Invitae is also making changes to UTA, we should coordinate.

andreasprlic commented 5 years ago

Hi Reece, yes we should definitely coordinate. One feature we were considering to add to UTA, is a utility to load custom-aligned transcripts into UTA. There are a few transcripts for which NCBI does not provide alignments to GRCh37, however they align perfectly. Would be nice if there was a simple way to add alignments for such cases. I should prob file a related UTA ticket for this, so we can discuss this in its own thread...

reece commented 5 years ago

See https://github.com/biocommons/uta/issues/220