scRNA-seq_analysis

tools/predict_by_classifier/predict.py

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+import sys
+args = sys.argv
+model_fname = args[1]
+data_fname = args[2]
+predictions_fname = args[3]
+pca_fname = args[4]
+
+import pickle
+import pandas as pd
+
+print("loading model ...")
+model = pickle.loads(open(model_fname, "rb").read())
+pca   = pickle.loads(open(pca_fname, "rb").read())
+
+print("loading data....")
+predictions = pd.read_csv(data_fname, sep = ",", index_col = 0).values
+print("classifying cells ... ")
+predictions = pca.transform(predictions);
+predictions = model.predict(predictions)
+print("writing results to disk...")
+df = pd.DataFrame(predictions)
+df.to_csv(predictions_fname)
+print("Classification finished. Python will now say goodbye. Handing over to R.")