Create get_gene_exp.py

utils/get_gene_exp.py

@@ -0,0 +1,43 @@
+import sys
+
+import numpy as np
+
+infile = sys.argv[1]
+expfile = sys.argv[2]
+outfile = sys.argv[3]
+
+genes = {}
+with open(infile, 'r') as f:
+    for line in f:
+        gene = line.split('|')[5]
+        expressions = [int(x) for x in line.strip().split()[1:]]
+        if (gene in genes):
+            genes[gene].append(expressions)
+        else:
+            genes.update({gene:[expressions]})
+
+expnames = []
+with open(expfile, 'r') as f:
+    for line in f:
+        expnames.append(line.strip())
+
+with open(outfile, 'w') as o:
+    o.write("gene\t")
+    for i in range(len(expnames) - 1):
+        o.write(expnames[i])
+        o.write("\t")
+    o.write(expnames[len(expnames) - 1])
+    o.write("\n")
+    for gene in genes.keys():
+        o.write(gene)
+        o.write("\t")
+        mean_exp = np.array(genes[gene])
+        print(mean_exp)
+        mean_exp = np.mean(mean_exp, axis = 0)
+        print(gene, mean_exp)
+        for k in range(len(mean_exp) - 1):
+            o.write(str(round(mean_exp[k])))
+            o.write("\t")
+        o.write(str(round(mean_exp[len(mean_exp) - 1])))
+        o.write("\n")
+