scRNA-seq_analysis

pipelines/93_gene_grouping/clustering.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Jan 15 20:52:21 2019
+
+@author: doru
+"""
+
+import sys
+from os.path import join
+import pandas as pd
+import numpy as np
+
+args = sys.argv
+output_folder = args[1]
+no_clusters = int(args[2])
+
+expression_file = join(output_folder, "expression.csv")
+expression_df = pd.read_csv(expression_file, index_col = 0)
+expression      = np.transpose(expression_df.values)
+
+from sklearn.mixture import GaussianMixture
+clustering = GaussianMixture(n_components = no_clusters, random_state = 19).fit(expression)
+clustering = clustering.predict(expression)
+
+# save the output
+gene_names = list(expression_df.head(0))
+df = {"GeneNames": gene_names, "Cluster": clustering}
+df = pd.DataFrame.from_dict(df)
+
+df.to_csv(join(output_folder, "clustering.csv"))