Updates paths

cvxgrp · Dec 2, 2024 · 09df0df · 09df0df
1 parent a695c09
commit 09df0df
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/utils/cleanup_adelie_data.py b/utils/cleanup_adelie_data.py
@@ -5,10 +5,10 @@
 import pandas as pd
 import pgenlib as pg
 
-data_dir = "/oak/group/candes/for_parth"
-bedname = os.path.join(data_dir, "EUR_subset.bed")
-bimname = os.path.join(data_dir, "EUR_subset.bim")
-famname = os.path.join(data_dir, "EUR_subset.fam")
+data_dir = "/oak/stanford/groups/candes/for_parth"
+bedname = os.path.join(data_dir, "ukb_gen_british.bed")
+bimname = os.path.join(data_dir, "ukb_gen_british.bim")
+famname = os.path.join(data_dir, "ukb_gen_british.fam")
 
 df_fam = pd.read_csv(
     famname,

diff --git a/utils/sherlock_script.py b/utils/sherlock_script.py
@@ -9,9 +9,9 @@
 if len(sys.argv) != 2:
     raise RuntimeError()
 
-data_dir = "/oak/group/candes/for_parth"
+data_dir = "/oak/stanford/groups/candes/for_parth"
 cache_dir = "/scratch/candes/for_parth"
-df = pd.read_csv(os.path.join(data_dir, "master_phe.csv"), sep="\t", index_col=0)
+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()