Added sorted outputs to improve handling in IGV

-> Fix #55

bin/3.1_create_gtf/Modules/Validator.py

@@ -1,7 +1,10 @@
+import os
+
+
 class Validator:
 
     """
-        Class to validate the gtf-output-file.
+        Class to validate and sort the gtf-output-file.
         @author: Sebastian Beyvers
         @contact: sebastian.beyvers@med.uni-giessen.de
 
@@ -13,8 +16,17 @@ def __init__(self, out_file):
         # input_parameter: out_file = path to output file
 
         self.out_file = out_file
+        self.sort_file()
         self.test_read_file()
 
+    def sort_file(self):
+
+        # function that utilizes linux sort to sort the output by chromosome and start coordinate,
+        # this improves handling in tools like IGV
+
+        command = "sort -V -k1,1 -k4,4n -o "+self.out_file+" "+self.out_file
+        os.system(command)
+
     def test_read_file(self):
 
         # Method to test the output file-format