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Getting error TypeError: unhashable type: 'SeqFeature' #60

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nachodeq opened this issue Oct 23, 2023 · 1 comment
Open

Getting error TypeError: unhashable type: 'SeqFeature' #60

nachodeq opened this issue Oct 23, 2023 · 1 comment

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@nachodeq
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While trying to run a full annotate + dn/ds:

python3 /home/pseudofinder/pseudofinder.py annotate --genome X.gbk --reference Y.gbk --database /home/plasmidfinder_db/DB.fasta --outprefix X

Im getting the following error:

/home/.local/lib/python3.10/site-packages/Bio/SeqFeature.py:257: BiopythonDeprecationWarning:

Using the strand argument is deprecated, and will be removed in a future release. Please set it via the location object instead.

Traceback (most recent call last):
File "/home/pseudofinder/pseudofinder.py", line 42, in
annotate.main()
File "/home/pseudofinder/modules/annotate.py", line 1116, in main
proteome = extract_features_from_genome(args, genome, 'CDS')
File "/home/pseudofinder/modules/annotate.py", line 192, in extract_features_from_genome
feature_list = list(set(feature_list))
TypeError: unhashable type: 'SeqFeature'

Seems to be a problem with BioPython but I cannot find any container with the previous version of pseudofinder containing the needed version of biopython.
Any help would be appreciated.

Thanks in advance!

@nachodeq
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Fixed installing biopython 1.79 in the pseudofinder env.

For anyone having the same problem just activate your environment and do:

pip install biopython==1.79

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