--- a/mutation_analysis.py	Wed Jul 13 08:04:13 2016 -0400
+++ b/mutation_analysis.py	Wed Jul 13 09:04:15 2016 -0400
@@ -146,35 +146,6 @@
 			absentAAbyID[c] -= 1
 		o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in absentAAbyID]) + "\n")
 
-
-
-aa_mutations_file = outfile[:outfile.rindex("/")] + "/aa_mutations.txt"
-with open(aa_mutations_file, 'w') as o:
-	o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
-	o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation[1:]]) + "\n")
-	o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")
-
-
-aa_mutations_file_ca = outfile[:outfile.rindex("/")] + "/aa_mutations_ca.txt"
-with open(aa_mutations_file_ca, 'w') as o:
-	o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
-	o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["ca"][1:]]) + "\n")
-	o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")
-
-
-aa_mutations_file_cg = outfile[:outfile.rindex("/")] + "/aa_mutations_cg.txt"
-with open(aa_mutations_file_cg, 'w') as o:
-	o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
-	o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["cg"][1:]]) + "\n")
-	o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")
-
-
-aa_mutations_file_cm = outfile[:outfile.rindex("/")] + "/aa_mutations_cm.txt"
-with open(aa_mutations_file_cm, 'w') as o:
-	o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
-	o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["cg"][1:]]) + "\n")
-	o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")
-
 if linecount == 0:
 	print "No data, exiting"
 	with open(outfile, 'w') as o: