diff phyloconversion/prune_phytab_using_list.py @ 0:5b9a38ec4a39 draft default tip

First commit of old repositories

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloconversion/prune_phytab_using_list.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,31 @@
+#!/usr/bin/python -tt
+            
+##usage: ./pullgoodseqs.py <originalphytab> <bls2remove> <keep|discard> > outfile
+#import modules
+import sys, os, numpy, re
+
+def read(filename):
+  f = open(filename)
+  bad = open(sys.argv[2])
+  lines = f.readlines()
+  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:
+#    line.strip()
+     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()