Added script to batch queries to primer3 from a multifasta file.

batch_primer3.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+
+from query_primer3 import query_primer3
+import fasta
+import sys
+import re
+import os
+
+if len(sys.argv) < 2:
+    print "Usage: %s multi_fasta PRIMER3_ARG=VALUE..."
+
+mfas = fasta.read_from(sys.argv[1])
+primer3args = sys.argv[2:]
+
+bad_chr = re.compile("[^a-zA-Z0-9_-]")
+
+basedir, basename = os.path.split(sys.argv[1])
+
+for i, s in enumerate(mfas):
+    out = os.path.join(basedir, bad_chr.sub('_', s.header) + '.primer3')
+    print '[%i/%i]' % (1 + i, len(mfas)), "Querying", s.header
+    query_primer3(['SEQUENCE=' + s.sequence, '-o', out] + primer3args)