GenoTools: Advanced Genotype Data Analysis A robust suite for processing genotype data, offering genotype calling (.idat to PLINK), comprehensive sample/variant QC, and ancestry estimation. Ideal for computational biology and genetics research.
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Adjust gwas module to allow for any phenotype (not just PHENO1) #172
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.')