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phglab / ALFATClust

Biological sequence clustering tool with dynamic threshold
GNU General Public License v3.0
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Fix 'format' for newer biopython versions #2

Closed boneta closed 2 years ago

boneta commented 2 years ago

Hi!

I just found myself facing the same error message that @mmpust describes at #1.

Changes in the last version of Biopython (v1.79) has modified the way the format method for a sequence alignment behaves. From now on, the 'fasta' argument is no longer recognized as a valid format and will rise an exception. Some of the documentation is still old, but the new implementation can be checked.

Removing the 'fasta' argument will fix this issue. And I have tested that it remains retro-compatible with Biopython v1.78, as it falls-back to 'fasta' when no argument is provided.

jimmykhchiu commented 2 years ago

Hi @boneta, thanks for your information.

I am currently updating ARGDIT (which I also need to modify the codes to use latest Biopython as well). Will get back to this after I finish the update.