--- a/rename.py	Thu Jul 26 13:02:23 2018 -0400
+++ b/rename.py	Thu Jul 26 15:46:24 2018 -0400
@@ -1,6 +1,6 @@
 """
 Call rename to rename scaffolds in reference genome so that the sequence names are less than 31 characters. Rename all scaffolds to scaffold_1, scaffold_2, ..., scaffold_N and provide a name mapping file
-Call truncate to truncate the scaffold names that are more than 31 characters. Replace non-ASCII character with '_'
+Call truncate to truncate the scaffold names that are more than 31 characters. Replace each invalid character (non-ASCII, '\t', '\n', '\x0b', '\x0c', '\r') with '_'
 """
 import sys
 import csv
@@ -21,7 +21,7 @@
                     writer.writerow([oldname.encode('utf-8'), newname])
                 out.write(line)
 
-def truncate(inputFile, outputFile):
+def truncate(inputFile, outputFile, valid_characters):
     names = []
     with codecs.open(outputFile, 'w', encoding='utf-8') as out:
         with codecs.open(inputFile, 'r', encoding='utf-8') as rf:
@@ -30,7 +30,7 @@
                 if ">" in l:
                     print l.encode('utf-8')
                     name = l[1:].rstrip()
-                    name = substituteNonAscii(name)
+                    name = substituteNonAscii(name, valid_characters)
                     if len(name) > 31:
                         name = name[:31]
                         print "\tTruncate the scaffold name to less than 31 characters: %s" % name
@@ -41,11 +41,11 @@
                     print "======================\n"
                 out.write(l)
 
-def substituteNonAscii(str):
+def substituteNonAscii(str, valid_charaters):
     l = []
     for c in str:
-        if c not in string.printable:
-            print "\tSubstitute Non-ASCII character %s with _" % c.encode('utf-8')
+        if c not in valid_charaters:
+            print "\tSubstitute invalid character %s with _" % c.encode('utf-8')
             c = '_'
         l.append(c)
     return "".join(l)
@@ -54,13 +54,14 @@
     inputfile = str(sys.argv[1])
     manipulate = str(sys.argv[2])
     outputfile = str(sys.argv[3])
+    valid_characters = string.letters + string.punctuation + string.digits + ' '
     if manipulate == "rename":
         indexfile = str(sys.argv[4])
         csvfile = open(indexfile, 'w')
         writer = csv.writer(csvfile)
         rename(inputfile, outputfile, writer)
     elif manipulate == "truncate":
-        truncate(inputfile, outputfile)
+        truncate(inputfile, outputfile, valid_characters)
 
 if __name__ == "__main__":
     main()