Add allcop predictions file

Molmed · Oct 15, 2024 · 5586ead · 5586ead
1 parent 6bd7962
commit 5586ead
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diff --git a/src/mpm_experiments/__init__.py b/src/mpm_experiments/__init__.py
diff --git a/src/mpm_experiments/allcop_predictions.py b/src/mpm_experiments/allcop_predictions.py
@@ -0,0 +1,16 @@
+import pandas as pd
+from src.allium.gex_classifier import GEXClassifier
+
+datasets = ['jude', 'lilljebjorn', 'jude']
+data_dir = '/home/mariya/Data/allium'
+gc = GEXClassifier('v3')
+
+for dataset in datasets:
+    print("Predicting for", dataset)
+    testX = pd.read_csv(f'{data_dir}/{dataset}.counts.allium.csv',
+                        index_col="id")
+    pheno = pd.read_csv(f'{data_dir}/{dataset}.pheno.allium.csv',
+                        index_col="id",
+                        sep=';')
+    result = gc.get_predictions(testX, pheno=pheno)
+    result.to_csv(f'{data_dir}/{dataset}.predictions.csv')