continue
    num_snps_skipped += 1
    samp_id = sline[id_index]
    ref_allele = sline[ref_allele_index]
    tum_allele = sline[tum_allele_index]
    snp = ref_allele + tum_allele
    if not snp in transitions:
        snp = nucleotide_complement[ref_allele] + nucleotide_complement[tum_allele]
    ref_trinuc = sline[ref_tri_index]
    if ref_trinuc == "NA":
        print "Warning: Reference allele not available on "+
                "line %d; skipping line"%line_number
        continue
    if not ref_trinuc[1] == snp[0]:
        print "Warning: Reference allele does not match reference "+
                "trinucleotide; skipping line %d"%line_number**
        continue
    snp_with_ctx = ref_trinuc[0] + snp + ref_trinuc[2]
    if not samp_id in signatures:
        signatures[samp_id] = [0 for i in substitution_order]
    if snp_with_ctx not in substitution_order:
        print "Warning: substitution on line " +
                "%d is %s, not "%(line_number,snp_with_ctx) +
                "found among possible substitutions. Skipping line."

Traceback (most recent call last):
  File "main.py", line 59, in <module>
    signatures = signature.make(args.in_file, substitution_order=stratton['substitution_order'], out_path = args.spectrum_output)
  File "/home/ateeqanees/Mutation/centos/mutation-signatures-master/signature.py", line 73, in make
    if not ref_trinuc[1] == snp[0]:
IndexError: string index out of range