Biopython Project

Open-source bioinformatics libraries in Python

[Biopython Project @Biopython]

We don't have a dedicated Mastodon account, for now keep an eye on https://t.co/GBy2MjmWdJ and #Biopython

[Biopython Project @Biopython]

We're following the OBF lead and not using Twitter anymore, see https://t.co/iuKMQkgSEM

And Biopython 1.82 has just been released, see https://t.co/l2sYg4DvHN

[Biopython Project @Biopython]

Way overdue, but Biopython 1.80 is out https://t.co/meHU0lYBc1 - expect formal announcement later https://t.co/Y0yFt6BLpm - conda packages soon too! Thank you to all the contributors /Peter

[Biopython Project @Biopython]

@webflags1 @NCBI Sounds like a planned change - and quite likely the NCBI did make an announcement somewhere (I’m not familiar with that particular DB) /Peter

[Biopython Project @Biopython]

@webflags1 @NCBI You’ll have to ask the NCBI - I’d suggest sharing the URL itself, the handle from Bio.Entrez has a .url attribute you can look at. You can also try debugging the URL in your browser (e.g. try other format/mode combinations). /Peter

[Peter Cock @pjacock]

Just ordered a pair of free 2FA keys courtesy Google Open Source Security Team for use with PyPI where a few of my projects are now deemed “critical” (plus @Biopython) https://t.co/xAmzfzcivm

[Martin Larralde @althonos]

55 lines of #Python code to build a Multiple Sequence Alignment viewer for the terminal with the #Rich library (from @textualizeio) #bioinformatics

[Biopython Project @Biopython]

@NEdgingtonPhD We’re deprecating the older Bio.pairwise2 in the next release.

[Biopython Project @Biopython]

@pjacock @tomeraltman Logged as https://t.co/wVKbOvvDzX

[Biopython Project @Biopython]

@chasewnelson @ThePSF Not really a Biopython thing, does feel like something the #Python #Pandas community could help with though? /Peter

[Biopython Project @Biopython]

@NWaglechner @kaiblin This was due to a change in GenBank files without an actual sequence are represented as of Biopython 1.79, see also deprecation of the UnknownSeq object https://t.co/it9MHVwSY4 /Peter

[Biopython Project @Biopython]

@KarenFlemingPhD Yes please - pull request via the “Edit on GitHub” link top left of that page would be most welcome. /Peter

[Biopython Project @Biopython]

@mglerner @KarenFlemingPhD @Python Commit https://t.co/PJYCh6SdZ4 should fix the doctest formatting on https://t.co/mtJsTmoSk2 (next time the HTML gets updated). If you spot anymore, please open an issue. Thanks /Peter

[Biopython Project @Biopython]

@kaiblin This will be the replacement for the UnknownSeq object I think? Could you log an issue please /Peter @pjacock

[Yu Kitago @uKitago]

#Biopython can handle #snapgene file! Using this feature, it's possible to easily convert many snapgene files into #genbank format files!!

[Biopython Project @Biopython]

NumPy has dropped Python 3.6 support, Biopython plans to soon. Any objections? https://t.co/Bos0Zkdkt1 https://t.co/AdpAKPqYKZ

[SonarCloud @SonarCloud]

Our #Python bug hunt in popular, well-maintained projects (@TensorFlow, numpy, salt, sentry and @Biopython) turned up interesting stuff like undefined var reference, unreachable code, and more.

https://t.co/hvtrcPlGVD

[Biopython Project @Biopython]

@BioIsaac6716 @numpy_team @ProjectJupyter No, you need to star them on GitHub too ;)

More seriously, have a look at the issue trackers for beginner or newcomer friendly issues if you want to contribute directly. /Peter

[Biopython Project @Biopython]

@EstadoAlternado @poikahmusica Glad you solved it. Yes, KeyError is expected when the key isn’t in the dictionary.

[Vini Salazar @vinisalazar_]

Very happy to have my first contribution to @Biopython merged today! Hope to contribute more in the future. Shoutout to @pjacock for the patience in reviewing my PR.

#opensource #python #bioinformatics