Fixes issues

cvxgrp · Dec 3, 2024 · 02ef295 · 02ef295
1 parent 47f3db3
commit 02ef295
Showing 1 changed file with 4 additions and 5 deletions.
diff --git 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)] +