Autopkgtest failure with new version of kaptive - may be related to new version of biopython

[Andreas Tille <andreas@an3as.eu>]

Hi,

the new version (0.7.3) of kaptive[1] fails its autopkgtest:

+ kaptive.py -a exact_match.fasta -k /usr/share/kaptive/reference_database/Klebsiella_k_locus_primary_reference.gbk -o output/test
/usr/lib/python3/dist-packages/Bio/GenBank/__init__.py:1287: BiopythonParserWarning: The NCBI states double-quote characters like " should be escaped as "" (two double - quotes), but here it was not: 'undecaprenyl-phosphate galactose phosphotransferase" glucose-1-phosphate transferase'
  warnings.warn(
Error: tblastn crashed!


Interestingly also the old version shows currently an issue in
testing on amd64[2]:

+ kaptive.py -a exact_match.fasta -k /usr/share/kaptive/reference_database/Klebsiella_k_locus_primary_reference.gbk -o output/test
Error: tblastn crashed!


But this seems to be kind of a random failure since unstable as well as
arm64 and ppc64el in testing are currently OK[3].

Kind regards

       Andreas.


[1] https://salsa.debian.org/med-team/kaptive
[2] https://ci.debian.net/data/autopkgtest/testing/amd64/k/kaptive/7000344/log.gz
[3] https://ci.debian.net/packages/k/kaptive/

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