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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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Proposal for compatibility with Biopython 1.78 #133

Closed emollier closed 3 years ago

emollier commented 3 years ago

Greetings,

Biopython 1.78 deprecated and removed the Bio.Alphabet module. I followed their recommendations on how to move forward, published on https://biopython.org/wiki/Alphabet and came up with this small change, so that srst2 can be compatible with this Biopython version as well.

Have a nice day, :) Étienne.

scwatts commented 3 years ago

Hi Étienne,

Thank you for the pull request, this looks good to me. We would also like to preserve backwards compatibility with older versions of biopython - there's some example code in the link you provided to do this.

If you can update your pull request to maintain compatibility with previous versions of biopython, we'll merge your commits asap.

Thanks, Stephen

emollier commented 3 years ago

Hi Stephen,

Stephen Watts, on 2020-11-10 16:21:21 -0800:

Thank you for the pull request, this looks good to me. We would also like to preserve backwards compatibility with older versions of biopython - there's some example code in the link you provided to do this.

This makes sense, I tried something with the file which needed the IUPAC unambiguous DNA and pushed the change. I tested on Biopython 1.73 and 1.78, and things seemed to work.

Kind Regards, -- Étienne Mollier etienne.mollier@mailoo.org Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/4, please excuse my verbosity.

scwatts commented 3 years ago

Hi Étienne, thanks for updating your pull request. I've looked into this some more and found that biopython dropped support for python2 in their 1.76 release, and so compatibility changes for biopython 1.78 in srst2 aren't currently applicable. However, srst2 may be ported to python3 in the future and we'll merge your changes if that happens but for now I'll close the pull request.