Describe the bug
gwas fails when trying to run with a phenotype that's not PHENO1
To Reproduce
attempt to run gwas with a column that is anything but PHENO1
Expected behavior
should be able to accept any phenotype column header
Screenshots
sys.exit(handle_main())
File "/gpfs/gsfs12/users/vitaled2/.venv/lib/python3.10/site-packages/genotools/main.py", line 117, in handle_main
args_dict = upfront_check(args_dict['geno_path'], args_dict)
File "/gpfs/gsfs12/users/vitaled2/.venv/lib/python3.10/site-packages/genotools/utils.py", line 125, in upfront_check
raise KeyError(f'{geno_path}.psam is missing PHENO1 column. Even if no PHENO1 information is present, GenoTools requires a PHENO1 column.')
Describe the bug
gwas fails when trying to run with a phenotype that's not PHENO1
To Reproduce
attempt to run gwas with a column that is anything but PHENO1
Expected behavior
should be able to accept any phenotype column header
Screenshots
sys.exit(handle_main())
File "/gpfs/gsfs12/users/vitaled2/.venv/lib/python3.10/site-packages/genotools/main.py", line 117, in handle_main
args_dict = upfront_check(args_dict['geno_path'], args_dict)
File "/gpfs/gsfs12/users/vitaled2/.venv/lib/python3.10/site-packages/genotools/utils.py", line 125, in upfront_check
raise KeyError(f'{geno_path}.psam is missing PHENO1 column. Even if no PHENO1 information is present, GenoTools requires a PHENO1 column.')