allow to process gzipped or plain input files

generate.py

@@ -65,16 +65,30 @@ output = open(output_file_unsorted, "w")
 
 print('Generating bed file: ' + output_file_unsorted)
 
-with gzip.open(inputFile, 'rt') as hIN:
-    for line in hIN:
-        F = line.rstrip('\n').split('\t')
-        output_line = transform(F)
-        if output_line[0] in chromosomes:
-            print("\t".join(output_line), file=output)
-        else:
-            if not output_line[0] in unkown_chromosomes:
-                print("Unknown chromosome '" + output_line[0] + "'")
-            unkown_chromosomes[output_line[0]] = True
+if inputFile.endswith('gz'):
+    with gzip.open(inputFile, 'rt') as hIN:
+        for line in hIN:
+            F = line.rstrip('\n').split('\t')
+            output_line = transform(F)
+            if output_line[0] in chromosomes:
+                print("\t".join(output_line), file=output)
+            else:
+                if not output_line[0] in unkown_chromosomes:
+                    print("Unknown chromosome '" + output_line[0] + "'")
+                unkown_chromosomes[output_line[0]] = True
+else:
+    with open(inputFile) as f:
+        lines = f.readlines()
+        for line in lines:
+            F = line.rstrip('\n').split('\t')
+            output_line = transform(F)
+            if output_line[0] in chromosomes:
+                print("\t".join(output_line), file=output)
+            else:
+                if not output_line[0] in unkown_chromosomes:
+                    print("Unknown chromosome '" + output_line[0] + "'")
+                unkown_chromosomes[output_line[0]] = True
+
 output.close()
 
 if not Path('bin').is_dir():