--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenies/prune_phytab_using_list.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,38 @@
+#!/usr/bin/python -tt
+            
+##usage: ./prune_phytab_using_list.py <originalphytab> <bls2remove> <keep|discard> > outfile
+
+#import modules
+import sys, os, numpy, re
+
+def read(filename):
+  f = open(filename)
+  lines = f.readlines()
+  # for case where list is an empty file (here, under 20 bytes)
+  if os.lstat(sys.argv[2]).st_size < 20: 
+    for line in lines:
+      print line,
+  else:
+    bad = open(sys.argv[2]) 
+    badlines = bad.readlines()
+    badstripped = [line[:-1] for line in badlines]
+    str1 = '|'.join(badstripped)
+    str2 = '('+str1[:-1]+')'  
+    pattern = re.compile(str2)
+    count=0
+    for line in lines:
+      match = pattern.findall(line)
+      if match and sys.argv[3] == 'keep':
+        print line,
+      if not match and sys.argv[3] == 'discard':
+        print line,
+    bad.close()
+  f.close()
+
+def main():
+  read(sys.argv[1])
+
+if __name__ == '__main__':
+  main()
+
+