Latest biopython version breaks Alphabet dependency

[johnstonmj]

I encountered the error: ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information

This seems to have changed with biopython 1.78 Installing biopython=1.77 fixed this issue for me.

Perhaps update the conda recipe to specify biopython=1.77?

[iprada]

Hi John!

Thanks for reporting! and thanks for solving it. I am very busy right now, and you have made my life easier. This are the best type of issues I can get. I will update the bioconda recipe tomorrow.

Best,

Iñigo

[kpkhushi15]

I encountered the error: ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify themolecule_typeas an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information

This seems to have changed with biopython 1.78 Installing biopython=1.77 fixed this issue for me.

Perhaps update the conda recipe to specify biopython=1.77?

Hi John! I encountered the same issue. After seeing your post I changed the biopython version==1.77 and now error got fixed. I am able to run the commands successfully.

Thankx for posting this issue.