--- a/mutation_analysis.py	Wed Apr 01 05:26:52 2015 -0400
+++ b/mutation_analysis.py	Thu Apr 02 03:31:23 2015 -0400
@@ -72,6 +72,7 @@
 aggctatIndex = 0
 atagcctIndex = 0
 first = True
+IDlist = []
 with open(infile, 'r') as i:
 	for line in i:
 		if first:
@@ -93,6 +94,7 @@
 		WRCYCount[ID] = sum([1 for (x,y,z) in WRCY if z and z != "CDR3" and any([(x <= int(where) <= y) for (frm, where, to, a,b,c,d) in mutationdic[ID + "_" + z]])])
 		WACount[ID] = sum([1 for (x,y,z) in WA if z and z != "CDR3" and any([(x <= int(where) <= y) for (frm, where, to, a,b,c,d) in mutationdic[ID + "_" + z]])])
 		TWCount[ID] = sum([1 for (x,y,z) in TW if z and z != "CDR3" and any([(x <= int(where) <= y) for (frm, where, to, a,b,c,d) in mutationdic[ID + "_" + z]])])
+		IDlist += [ID]
 
 
 directory = outfile[:outfile.rfind("/") + 1]
@@ -124,3 +126,20 @@
 		y = valuedic["total"]
 		z = str(round(x / float(valuedic["total"]) * 100, 1))
 		o.write("," + str(x) + "," + str(y) + "," + z + "\n")
+
+
+#for testing
+seq_motif_file = outfile[:outfile.rindex("/")] + "/motif_per_seq.txt"
+first = True
+with open(seq_motif_file, 'w') as o:
+	for ID in IDlist:
+		if first:
+			o.write("ID\tRGYWC\tWRCY\tWA\tTW\n")
+			first = False
+			continue
+		print ID
+		print RGYWCount[ID]
+		print WRCYCount[ID]
+		print WACount[ID]
+		print TWCount[ID]
+		o.write(ID + "\t" + str(RGYWCount[ID]) + "\t" + str(WRCYCount[ID]) + "\t" + str(WACount[ID]) + "\t" + str(TWCount[ID]) + "\n")