Replace extractcounts.py

scripts/extractcounts.py

@@ -50,7 +50,9 @@ def group_replicates(sample_names):
     with open(sample_names) as f_names:
         for f in f_names:
             f = f.strip("\n")
-            rep_dict_key = f[:-5]
+            # strip redundant info out of string
+            fn = f[:-4].split('-')
+            rep_dict_key = fn[0] + fn[1][0:3]+ fn[1][4:]
             if not rep_dict_key in rep_dict:
                 rep_dict[rep_dict_key] = {}
             rep_dict[rep_dict_key][f] = parse_gtf('samples/'+ str(f))
@@ -107,4 +109,5 @@ def main(ref_name, sample_names):
 
 # Run script
 if __name__ == "__main__":
-    main(argv[1], argv[2])
\ No newline at end of file
+    #main(argv[1], argv[2])
+    print(group_replicates(argv[1]))
\ No newline at end of file