Comments (3)
Hi!
I'm trying to use
vk primer
to design some primers and running into an importError with Bio.Alphabet:vk primer snip --ref=WBcel235 data/test.vcf.gz Traceback (most recent call last): File "/anaconda3/envs/vcf-kit/lib/python3.7/site-packages/vcfkit/primer.py", line 26, in <module> from vcfkit.utils.primer_vcf import primer_vcf File "/anaconda3/envs/vcf-kit/lib/python3.7/site-packages/vcfkit/utils/primer_vcf.py", line 11, in <module> from vcfkit.utils.primer3 import primer3 File "/anaconda3/envs/vcf-kit/lib/python3.7/site-packages/vcfkit/utils/primer3.py", line 9, in <module> from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA as DNA_SET File "/anaconda3/envs/vcf-kit/lib/python3.7/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.
I tried simply commenting out the Bio.Alphabet line from the files, but then I get a core dump instead of an output. Do you have suggestions on a better way to get around this error? I installed vcf-kit using the instructions on the GitHub front page.
Thank you!
Since biopython 1.78, Bio.Alphabet was removed, I think downgrade biopython to an older version will solve this.
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I recommend using the dockerized version of vcf-kit:
docker run -it andersenlab/vcf-kit vk primer
Unfortunately I cannot always keep up with changing python dependencies, but the docker image is much more static and should work.
Please let me know if you run into issues.
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Thank you both for your helpful replies!
I ended up using the Docker container with singularity and it's been working great.
singularity pull docker://andersenlab/vcf-kit
singularity run --fakeroot --writable vcf-kit_latest.sif
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