def main():
filename, pattern , alphabet = parse_args(sys.argv)
t = read_genome(filename)
p_bm = BoyerMoore(pattern, alphabet)
occurences, character_comparison_total, alignmnets_tried = boyer_moore(pattern, t, n)
print(" The pattern matches the genome %d times at locations %s " % (len(occurences), occurences))
print(" alignments tried: %d, character comparisons: %d" % (alignmnets_tried, character_comparison_total))
def main():
filename, barcode_file, mismatch = parse_args(sys.argv)
reference_file = read_genome(filename)
barcodes = read_barcodes(barcode_file)
barcode_count = count_barcodes_v2(barcodes, reference_file, mismatch)
write_to_csv("%s_result.csv" % filename, barcode_count)
print(" Table of barcodes %s " % (barcode_count))
def main():
filename, pattern = parse_args(sys.argv)
reference_genome = read_genome(filename)
#f.close() opened in utils, should I close it in utils?????
occur, occur_rc = naive_rc(pattern, reference_genome)
print(" The pattern matches the genome at locations %s " % occur)
print(" The RC matches the genome at locations %s " % occur_rc)
print("Occurences: %d, Occurences in RC: %d, Total: %d" %
(len(occur), len(occur_rc), (len(occur) + len(occur_rc))))
def main():
filename, pattern, mismatch = parse_args(sys.argv)
t = read_genome(filename)
all_matches, index_hits = approximate_match(pattern, t, mismatch)
print("there are %d exact macthes and %d index hits. Hit locations: %s" %
(len(all_matches), index_hits, all_matches))
def main():
filename, pattern, mismatch = parse_args(sys.argv)
reference_genome = read_genome(filename)
result, character_comparison_total, alignmnets_tried = naive(pattern, reference_genome, mismatch)
print(" The pattern matches the genome %d times at locations %s " % (len(result), result))
print(" alignments tried: %d, character comparisons: %d" % (alignmnets_tried, character_comparison_total))
def main():
filename, pattern = parse_args(sys.argv)
reference_genome = read_genome(filename)
#f.close() opened in utils, should I close it in utils?????
result = naive(pattern, reference_genome)
print(" The pattern matches the genome %d times at locations %s " % (len(result), result))