milw
commented
3 years ago apparently you need to specify both --cngb_metadata
Open tushar-ahmed opened 4 years ago
milw
commented
3 years ago apparently you need to specify both --cngb_metadata
(base) d3w@d3w:~/covseq$ python3 preprocess/concatenate_fasta.py -i TRIAL/ -o TRIAL/test.fasta --gisaid_metadata gisaid_hcov19.xls #########################
Concatenate all FASTA
######################### Input: TRIAL/ Output: TRIAL/test.fasta Traceback (most recent call last): File "preprocess/concatenate_fasta.py", line 79, in
main()
File "/home/d3w/.local/lib/python3.7/site-packages/click/core.py", line 829, in call
return self.main(args, kwargs)
File "/home/d3w/.local/lib/python3.7/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/d3w/.local/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/home/d3w/.local/lib/python3.7/site-packages/click/core.py", line 610, in invoke
return callback(args, **kwargs)
File "preprocess/concatenate_fasta.py", line 74, in main
cngb_id_map = get_cngb_id_map(cgnb_metadata)
File "preprocess/concatenate_fasta.py", line 11, in get_cngb_id_map
with open(in_fn) as f:
TypeError: expected str, bytes or os.PathLike object, not NoneType
I am facing this issue. help please
NB: I have installed python dependencies in conda environment.