gene body coordinates

Author: Kate Weaver

data/RNAseq/split_sets/save_gene_body_coords.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python3
+
+import sys
+import numpy as np
+
+#usage:
+'''
+./save_gene_body_coords.py rnaTPM_train_pc.txt 19012 trainGeneCoords_pc.npz
+./save_gene_body_coords.py rnaTPM_test_pc.txt 1967 testGeneCoords_pc.npz
+./save_gene_body_coords.py rnaTPM_ref_pc.txt 857 refGeneCoords_pc.npz
+'''
+
+input_file = sys.argv[1]
+tssN = int(sys.argv[2])
+
+to_save = np.zeros((tssN, 3), dtype=np.object)
+
+for i, line in enumerate(open(input_file)):
+    fields = line.strip('\r\n').split()
+    if i != 0:
+        to_save[i-1,0] = fields[0] #set chr
+        to_save[i-1,1] = int(fields[1]) #set "start", but really just the minimum gene body edge value
+        to_save[i-1,2] = int(fields[2]) #set "end", but really just the maximum gene body edge value
+
+output_file = sys.argv[3]
+f = open(output_file, 'wb')
+np.savez(f, geneBodyCoords = to_save)
+f.close()