parse annotation error
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TimHHH commented
Hi. I am getting this error in the log:
---[ parse annotation ]---
Command:
parse_annotation.py Results/./test02/NC-000962-3-H37Rv_mutated_1.30_annotation.txt NC-000962-3-H37Rv_mutated_1.30 /home/shared_data_ghi/CWGSMTB/Software/resetqtb-uvp/uvp/data/mutation_loci.txt
Standard Error:
Traceback (most recent call last):
File "/home/shared_data_ghi/CWGSMTB/Software/venv_resetqtb-uvp/bin/parse_annotation.py", line 7, in <module>
exec(compile(f.read(), __file__, 'exec'))
File "/home/shared_data_ghi/CWGSMTB/Software/resetqtb-uvp/scripts/parse_annotation.py", line 5, in <module>
from string import join
ImportError: cannot import name 'join' from 'string' (/home/shared_data_ghi/CWGSMTB/Software/venv_resetqtb-uvp/lib/python3.8/string.py)
The resulting *_Final_annotation.txt file is then empty and hence ---[ vcf_parser ]--- then also fails.
Thanks.
Tim