error with find_mutants

[EricFournier3]

Hi,

I'm using version 1.1.28 and I got the following error when running

alcov find_mutants samples.txt

Searching for mutations in None
Traceback (most recent call last):
File "/data/soft/anaconda/2021-11/envs/alcov/bin/alcov", line 8, in
sys.exit(main())
File "/data/soft/anaconda/2021-11/envs/alcov/lib/python3.7/site-packages/alcov/command_line.py", line 6, in main
fire.Fire(alcov.CovBreakdown)
File "/data/soft/anaconda/2021-11/envs/alcov/lib/python3.7/site-packages/fire/core.py", line 143, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/data/soft/anaconda/2021-11/envs/alcov/lib/python3.7/site-packages/fire/core.py", line 482, in _Fire
target=component.name)
File "/data/soft/anaconda/2021-11/envs/alcov/lib/python3.7/site-packages/fire/core.py", line 693, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/data/soft/anaconda/2021-11/envs/alcov/lib/python3.7/site-packages/alcov/init.py", line 21, in find_mutants
find_mutants(samples_path, mutations_path=mutations_path, min_depth=min_depth, save_img=save_img, csv=csv)
File "/data/soft/anaconda/2021-11/envs/alcov/lib/python3.7/site-packages/alcov/analyze.py", line 235, in find_mutants
with open(mutations_path, 'r') as f:
TypeError: expected str, bytes or os.PathLike object, not NoneType

I'm not sure if the mutations.txt file is mandatory in the command argument list. According to your README it is not

Thanks
Eric

[JennKnapp]

Hi Eric,

The mutations.txt file is not required for using the "find_mutants" function, but you do need to specify either a mutations.txt file (containing a list of mutations to look for) or a name of a lineage (then the tool will look for all mutations in the constellation for that lineage in your samples). When specifying a lineage make sure you are using the same name as the names of the constellation files found in"alcov/alcov/data/constellations/".

For example you can run:
alcov find_mutants samples.txt mutations.txt
or
alcov find_mutants samples.txt JN.1-like

I will update the README to reflect this, thank you!

Jenn

[EricFournier3]

Ok,
Thank you Jenn