Commit 84289edf authored by hjulienn's avatar hjulienn
Browse files

DEBUG: remove filter when saving results

parent 3b326494
...@@ -20,5 +20,5 @@ def filter_output(zscores, fout, R2_threshold = 0.6, minimum_ld = 5): ...@@ -20,5 +20,5 @@ def filter_output(zscores, fout, R2_threshold = 0.6, minimum_ld = 5):
chr_fo = zscores[['index', 'pos', 'A0', 'A1', 'Z', 'Var', "ld_score"]] chr_fo = zscores[['index', 'pos', 'A0', 'A1', 'Z', 'Var', "ld_score"]]
chr_fo["imputation_R2"] = 1-chr_fo["Var"] chr_fo["imputation_R2"] = 1-chr_fo["Var"]
chr_fo.columns = ['rsID','pos','A0','A1','Z', 'Var', "ld_score", "imputation_R2"] chr_fo.columns = ['rsID','pos','A0','A1','Z', 'Var', "ld_score", "imputation_R2"]
#loc[(chr_fo.Var < (1-R2_threshold)) & (chr_fo.ld_score > minimum_ld)]
chr_fo.loc[(chr_fo.Var < (1-R2_threshold)) & (chr_fo.ld_score > minimum_ld)].to_csv(fout, sep="\t", index=False) chr_fo.to_csv(fout, sep="\t", index=False)
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