Biopython Project

We don't have a dedicated Mastodon account, for now keep an eye on @OpenBio" target="_blank" rel="nofollow noopener">genomic.social/@OpenBio and #Biopython

We're following the OBF lead and not using Twitter anymore, see open-bio.org/2023/11/20/lea… And Biopython 1.82 has just been released, see open-bio.org/2023/12/22/bio…

Way overdue, but Biopython 1.80 is out pypi.org/project/biopyt… - expect formal announcement later mailman.open-bio.org/pipermail/biop… - conda packages soon too! Thank you to all the contributors /Peter

@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 @NCBI Thanks Peter for your reply! Waiting a for a response from the NCBI, but we may have a fix. It seems like they have quietly turned off support for the ipg rettype, but that ipg is now a db in itself that can be searched with a protein accession.

We're getting unexpected output for @NCBI API identical protein group records via @Biopython Entrez.efetch(db="protein", id=accession_nr, rettype="ipg", retmode="xml") Anyone know what's going on?

@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

@NCBI @Biopython specifically, the output is returned in genbank format instead of the ipg format requested

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) pypi.org/security-key-g…

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

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

@pjacock @tomeraltman Logged as github.com/biopython/biop…

@tomeraltman @Biopython Probably we just need to define __sub__ in a few places…

TIL that you can do basic interval arithmetic in @Biopython, such as translating a feature's location by a fixed amount. Addition is straight-forward, but subtraction is roundabout: `loc + (-5)` instead of `loc - 5`.

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

@ThePSF @Biopython The only way I can imagine, which is a bit cumbersome, is to: 1) create firstColList — a list of the columns to be placed in front 2) create a list of the remaining cols using a set difference, perhaps list(myDataFrame.columns).difference(firstColList) 3) reassign the DataFrame

Using #RStats, it's possible to reorder columns as follows: dplyr::select(myDataFrame, colName1, colName2, everything()) Is there a simple way to do the same with #Python #pandas—namely, pull out some columns to the front and specify the remainder with an everything() function?

@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 open-bio.org/2021/06/03/bio… /Peter

@kaiblin @Biopython curious about this - why would you need to do this?

I just released version 0.1.2 of merge-gbk-records github.com/kblin/merge-gb…, a script to join multiple genbank records into one with a spacer sequence. Version 0.1.2 is a bugfix release to support the current @Biopython release.

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

.@Biopython How about a clearly worked example, including all the import lines, etc?

@mglerner @KarenFlemingPhD @Python Commit github.com/biopython/biop… should fix the doctest formatting on biopython.org/docs/dev/api/B… (next time the HTML gets updated). If you spot anymore, please open an issue. Thanks /Peter

@KarenFlemingPhD @Python Excellent! And yeah, smart quotes on a coding website was an unexpected choice.

Any #Biopython @python friends out there who can write a tutorial on how to use this module? biopython.org/docs/dev/api/B… Trying to do this in Jupyter. What I need is an actual worked example.

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

Ah, crud, the new Bio.Seq.UndefinedSequenceError in @Biopython 1.79 really kills our WGS record detection by moving the place we need to detect the error to a completely different place in the code base, and no way to do it while staying compatible to 1.78 or older 😞💔

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

NumPy has dropped Python 3.6 support, Biopython plans to soon. Any objections? github.com/biopython/biop… mailman.open-bio.org/pipermail/biop…

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. blog.sonarsource.com/sonarcloud-fin…

@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

So you're saying following @numpy_team @Biopython @ProjectJupyter doesn't automatically make me a bio-coder??!?

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

@poikahmusica @Biopython A friend already made me realize that the problem was actually that due to the format of one of my input files, I was selecting a key that was not inside the dictionary. Already fixed, thanks!

Am I stupid? I really can't understand why I can't print protein sequences to StdOut using #Biopython. I am just using a very simple loop, and I keep getting the same error which I have not been able to debug. WTF? PS: I already imported the proper Bio.Alphabet and everything

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