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Adjust gwas module to allow for any phenotype (not just PHENO1)

Open dvitale199 opened this issue 3 months ago • 0 comments

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.')

dvitale199 avatar Mar 28 '24 16:03 dvitale199