actually splitting now

bin/fastq2contigs

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+import os
+import re
+import sys
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument('fastq')
+parser.add_argument('output')
+parser.add_argument('-n', dest='non', help='nubmer NNNs to cut a fastq file',
+                    type=int, default=10)
+
+args = parser.parse_args()
+
+F =  open(args.fastq)
+G = open(args.output, 'w')
+
+splitter = re.compile('n{'+str(args.non)+',}', re.I)
+
+header = F.readline()
+assert(header[0] == '@')
+header = header[1:].split()[0]
+print 'header', header
+
+seq = []
+for line in F:
+    if line[0] == '+': break
+    seq.append(line.strip())
+seq = "".join(seq)
+print 'read %d nt' % len(seq)
+
+contigs = splitter.split(seq)
+for i, c in enumerate(contigs):
+    G.write(">%s_%s\n" % (header, i))
+    while c:
+        G.write("%s\n" % c[:80])
+        c = c[80:]
+
+print "wrote %d contigs to %s" %  (len(contigs), sys.argv[2])
+
+F.close()
+G.close()
+