--- a/rename.py	Mon Jun 25 15:29:18 2018 -0400
+++ b/rename.py	Thu Jul 26 13:02:23 2018 -0400
@@ -1,12 +1,15 @@
 """
 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 '_'
 """
 import sys
 import csv
+import codecs
+import string
 
 def rename(inputfile, outputfile, writer):
     with open(outputfile, 'w') as out:
-        with open(inputfile, 'r') as rf:
+        with codecs.open(inputfile, 'r', encoding='utf-8') as rf:
             lines = rf.readlines()
             i = 1
             for line in lines:
@@ -15,16 +18,49 @@
                     newname = "scaffold_" + str(i)
                     line = ">" + newname + "\n"
                     i = i+1
-                    writer.writerow([oldname, newname])
+                    writer.writerow([oldname.encode('utf-8'), newname])
                 out.write(line)
 
+def truncate(inputFile, outputFile):
+    names = []
+    with codecs.open(outputFile, 'w', encoding='utf-8') as out:
+        with codecs.open(inputFile, 'r', encoding='utf-8') as rf:
+            lines = rf.readlines()
+            for l in lines:
+                if ">" in l:
+                    print l.encode('utf-8')
+                    name = l[1:].rstrip()
+                    name = substituteNonAscii(name)
+                    if len(name) > 31:
+                        name = name[:31]
+                        print "\tTruncate the scaffold name to less than 31 characters: %s" % name
+                    if name in names:
+                        sys.exit("Name conflict! Name " + name + " already exist.")
+                    names.append(name)
+                    l = ">" + name + "\n"
+                    print "======================\n"
+                out.write(l)
+
+def substituteNonAscii(str):
+    l = []
+    for c in str:
+        if c not in string.printable:
+            print "\tSubstitute Non-ASCII character %s with _" % c.encode('utf-8')
+            c = '_'
+        l.append(c)
+    return "".join(l)
+
 def main():
     inputfile = str(sys.argv[1])
-    outputfile = str(sys.argv[2])
-    indexfile = str(sys.argv[3])
-    csvfile = open(indexfile, 'w')
-    writer = csv.writer(csvfile)
-    rename(inputfile, outputfile, writer)
+    manipulate = str(sys.argv[2])
+    outputfile = str(sys.argv[3])
+    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)
 
 if __name__ == "__main__":
     main()