--- methratio.py.orig	2012-04-10 20:54:39.000000000 +0200
+++ methratio.py	2012-08-16 10:54:42.000000000 +0200
@@ -1,4 +1,5 @@
-import sys, time, os, array, optparse
+#!/usr/bin/python
+import sys, time, os, array, optparse, re
 usage = "usage: %prog [options] BSMAP_MAPPING_FILES"
 parser = optparse.OptionParser(usage=usage)
 
@@ -128,26 +129,32 @@
 
 disp('writing %s ...' % options.outfile)
 ss = {'C': '+', 'G': '-'}
+trint = {'CG[ACGT]$':'CPG','C[ACT]G$':'CHG', r"C[ACT][ACT]":'CHH', r"[ACGT]CG":'CPG',r"C[AGT]G":'CHG',r"[AGT][AGT]G":'CHH' }
 fout = open(options.outfile, 'w')
-z95, z95sq = 1.96, 1.96 * 1.96
-fout.write('chr\tpos\tstrand\tcontext\tratio\ttotal_C\tmethy_C\tCI_lower\tCI_upper\n')
+
+fout.write('chr\tpos\tstrand\tcontext\tcoverage\tmethylated_C\tperc_methy_C\n')
 nc, nd, dep0 = 0, 0, options.min_depth
 for cr in sorted(depth.keys()):
     depthcr, methcr, refcr = depth[cr], meth[cr], ref[cr]
     for i, d in enumerate(depthcr):
+        if i < 2: continue
         if d < dep0: continue
         nc += 1
         nd += d
         m = methcr[i]
         if m == 0 and not options.meth0: continue
         ratio = float(m) / d
-        seq = refcr[i-2:i+3]
         strand = ss[refcr[i]]
-        pmid = ratio + z95sq / (2 * d)
-        sd = z95 * ((ratio*(1-ratio)/d + z95sq/(4*d*d)) ** 0.5)
-        norminator = 1 + z95sq / d
-        CIl, CIu = (pmid - sd) / norminator, (pmid + sd) / norminator
-        fout.write('%s\t%d\t%c\t%s\t%.3f\t%d\t%d\t%.3f\t%.3f\n' % (cr, i+1, strand, seq, ratio, d, m, CIl, CIu))
+        if strand == '-':
+            seq = refcr[i-2:i+1]
+        else:
+            seq = refcr[i:i+3]
+    
+        for k, v in trint.items():
+            if re.match(k,seq):
+                context=v
+
+        fout.write('%s\t%d\t%c\t%s\t%d\t%d\t%.2f\n' % (cr, i+1, strand, context, d, m, m*100/d))
 
 fout.close()
 disp('done.')