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CPTR-ReSeqTB / UVP

Mycobacterium tuberculosis next generation sequence analysis
MIT License
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parse annotation error #32

Open TimHHH opened 4 years ago

TimHHH commented 4 years ago

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