Biopython 1.78 not compatible because of Alphabet missing
besnarda opened this issue · 3 comments
Using ARIBA for gene detection, I tried to download the ncbi database with the following line
ariba getref ncbi out.ncbi
E-fetching 5795 genbank records from BioProject PRJNA313047 and writing to. This may take a while.
Traceback (most recent call last):
File "/appli/conda-env/bioinfo/ariba-2.14.6/bin/ariba", line 312, in <module>
args.func(args)
File "/appli/conda-env/bioinfo/ariba-2.14.6/lib/python3.6/site-packages/ariba/tasks/getref.py", line 11, in run
getter.run(options.outprefix)
File "/appli/conda-env/bioinfo/ariba-2.14.6/lib/python3.6/site-packages/ariba/ref_genes_getter.py", line 664, in run
exec('self._get_from_' + self.ref_db + '(outprefix)')
File "<string>", line 1, in <module>
File "/appli/conda-env/bioinfo/ariba-2.14.6/lib/python3.6/site-packages/ariba/ref_genes_getter.py", line 620, in _get_from_ncbi
from Bio.Alphabet import generic_dna
File "/appli/conda-env/bioinfo/ariba-2.14.6/lib/python3.6/site-packages/Bio/Alphabet/__init__.py", line 21, in <module>
"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."
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.
As reported there it seems to be because of Biopython 1.78.
I will try downgrading to Biopython 1.77 to see if it solves the issue.
Did this work for you? If possible, could you provide a few lines on how to downgrade biopython?
Sorry for the late response! In case you are still stuck:
It did work for the Alphabet issue, but i encountered other issues that I wasn't able to solve so I didn't explore this tool further.
I didn't made the downgrade myself so I can't point you how to do it for sure.
If you are using conda, I believe you can try (I have not try it though).
conda install Biopython=1.77