--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/renameSequences2.py	Thu Sep 05 09:04:56 2019 -0400
@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+### this version does not use st input!!!!
+# how to use:
+# renameSequences.py fasta.file true index.out prefix_length   # for paired sequences
+# renameSequences.py fasta.file false index.out prefix_length   # not paired sequences
+
+import sys
+paired = sys.argv[2] == "true"
+index = open(sys.argv[3], 'w')
+
+if len(sys.argv) == 4:
+    prefix = 0
+else:
+    prefix = int(sys.argv[4])
+
+if paired:
+    P = 2
+    suffix = "f\n"
+else:
+    P = 1
+    suffix = "\n"
+i = j = 0
+reader = open(sys.argv[1], mode='r')
+for oneline in reader:
+    if oneline == "":
+        continue
+    if oneline[0] == ">":
+        i += 1
+        j += 1
+        prefix_string = oneline[1:(1 + prefix)].strip()
+        if j == 1:
+            header = ">" + prefix_string + str(i) + suffix
+            index.write(oneline[1:].strip() + "\t" + prefix_string + str(i) +
+                        suffix)
+        if j == 2:
+            i -= 1
+            header = ">" + prefix_string + str(i) + "r\n"
+            index.write(oneline[1:].strip() + "\t" + prefix_string + str(i) +
+                        "r\n")
+        sys.stdout.write(header)
+        if j == P:
+            j = 0
+    else:
+        sys.stdout.write(oneline)
+index.close()