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AndersenLab / VCF-kit

VCF-kit: Assorted utilities for the variant call format
http://www.andersenlab.org
MIT License
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vk primer bio.alphabet error #35

Closed kimh11 closed 3 years ago

kimh11 commented 3 years ago

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!

SilenWang commented 3 years ago

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.

danielecook commented 3 years ago

@SilenWang @kimh11 -

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.

kimh11 commented 3 years ago

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