From 02ef295f032aef53809a232677d0a97b22a9a4c1 Mon Sep 17 00:00:00 2001 From: Parth Nobel Date: Mon, 2 Dec 2024 16:22:00 -0800 Subject: [PATCH] Fixes issues --- utils/sherlock_script.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/utils/sherlock_script.py b/utils/sherlock_script.py index cc8a129..9c86ed0 100644 --- a/utils/sherlock_script.py +++ b/utils/sherlock_script.py @@ -11,12 +11,11 @@ data_dir = "/oak/stanford/groups/candes/for_parth" cache_dir = "/scratch/candes/for_parth" -df = pd.read_csv(os.path.join(data_dir, "phenotypes.QC.britishonly.csv"), sep="\t", index_col=0) -covars_dense = df.iloc[:, :-1].to_numpy() -y = df.iloc[:, -1].to_numpy() +df = pd.read_csv(os.path.join(data_dir, "phenotypes.QC.britishonly.csv"), index_col=0) +covars_dense = df.loc[:, df.columns != 'height'].to_numpy() +y = df['height'].to_numpy() -# TODO: check this -chromosomes = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] +chromosomes = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] X = ad.matrix.concatenate( [ad.matrix.dense(covars_dense)] +