Be more clear if there is a problem calculating seq. identity

Currently, if there are duplicated files in the run (i.e. same file
in different folders) domain sequences will be appended twice and
the fasta parser will join them in one single sequence -increasing
that particular sequence's length.
This commit just warns the user and continues. In theory this should
still give correct results.

functions.py

@@ -243,7 +243,7 @@ def check_data_integrity(gbk_files):
     if duplication == True:
         print "There was duplication in the input files, if this is not intended remove them."
         cont = raw_input("Continue anyway? Y/N ")
-        if cont.lower() == "n":
+        if cont.lower() != "y":
             sys.exit()
             
 
@@ -309,12 +309,21 @@ def calc_perc_identity(seq1, seq2, spec_domain, spec_domain_nest, domain):
     matches = 0
     
     for pos in range(len(seq1)): #Sequences should have the same length because they come from an MSA
-        if seq1[pos] == seq2[pos]:
-            if seq1[pos] != "-":
-                matches += 1
+        try:
+            if seq1[pos] == seq2[pos]:
+                if seq1[pos] != "-":
+                    matches += 1
+                    length += 1
+            else:
                 length += 1
-        else:
-            length += 1
+        except IndexError:
+            print("\tWARNING: there was a problem in calc_perc_identity")
+            print("\t Most likely a mismatch in sequences' lengths: " + str(len(seq1)) + ", " + str(len(seq2)))
+            print("\t Domain: " + domain)
+            print("\t  Specific domain 1: " + spec_domain)
+            print("\t  Specific domain 2: " + spec_domain_nest)
+            print("\t trying to continue...")
+            return float(matches) / float(length), length    
 
     return float(matches) / float(length), length