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scripts_CNV/find_cnv_DE.py

+#! /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+
+#Attention : pour que ça fonctionne, il faut : sed -i 's/"//g' outrider.tsv
+import sys 
+import csv
+
+
+lines = [line.rstrip() for line in open(sys.argv[1])]
+header = lines[0].split()
+print(header)
+liste_dijarn = lines[0].split()[1:]
+matrice_count = {l.split()[0]: l.split()[1:] for l in lines[1:]}
+outrider_file = [line.rstrip() for line in open(sys.argv[2])]
+outrider_file = outrider_file[1:]
+
+#comparaison des listes de gènes outrider vs matrix.all.counts
+
+key_matrix = matrice_count.keys()
+keys_outrider = set()
+for line in outrider_file:
+	gene = line.split()[1]
+	keys_outrider.add(gene)
+	dijarn = line.split()[2]
+	position = liste_dijarn.index(dijarn)
+	count_norm = line.split()[8]
+	matrice_count[gene][position] = count_norm
+
+to_remove = list(set(key_matrix) - set(keys_outrider))
+
+for key in to_remove:
+	del matrice_count[key]
+
+		
+with open(sys.argv[3], "w" , newline='') as output_file:
+	writer = csv.writer(output_file, delimiter='\t')
+	writer.writerow(header)
+	for i in matrice_count:
+		to_write =[i]+ matrice_count[i]
+		writer.writerow(to_write)