def main(argv):
pam250 = table.scoring(argv[0])
lines = fasta.read_ordered(argv[1])
result = strings.local_alignment(lines[0], lines[1], pam250)
print result[0]
print '\n'.join(r.translate(None, '-') for r in result[1:])
def main(argv):
blosom62 = table.scoring(argv[0])
s, t = fasta.read_ordered(argv[1])
result = strings.affine_gap_alignment(s, t, blosom62)
print result[0]
print '\n'.join(result[1:])
def main(argv):
s, t = fasta.read_ordered(argv[0])
m, n = len(s), len(t)
T1 = strings.mismatch_alignment_table(s, t)
T2 = strings.mismatch_alignment_table(s[::-1], t[::-1])
total = 0
for i in xrange(1, m + 1):
for j in xrange(1, n + 1):
total += T1[i - 1][j - 1] + T2[m - i][n - j] + (
1 if s[i - 1] == t[j - 1] else -1)
print T1[m][n]
print total
def main(argv):
s, t = fasta.read_ordered(argv[0])
result = strings.fitting_alignment(s, t)
print result[0]
print '\n'.join(result[1:])
def main(argv):
s, t = fasta.read_ordered(argv[0])
print ' '.join(str(i) for i in strings.find_indices_of_subsequence(s, t))
def main(argv):
dna_strings = fasta.read_ordered(argv[0])
results = strings.quadruple_alignment(*dna_strings)
print results[0]
print '\n'.join(results[1:])
def main(argv):
strings = fasta.read_ordered(argv[0])
matrix = distance.p_matrix(strings)
print '\n'.join([' '.join(['%0.5f' % col for col in row]) for row in matrix])
def main(argv):
s, t = fasta.read_ordered(argv[0])
result = strings.semi_global_alignment(s, t)
print result[0]
print '\n'.join(r for r in result[1:])
def main(argv):
blosom62 = table.scoring(argv[0])
s, t = fasta.read_ordered(argv[1])
m, n = len(s), len(t)
print strings.alignment_table(s, t, blosom62)[m][n]
def main(argv):
s, t = fasta.read_ordered(argv[0])
m, n = len(s), len(t)
C = strings.longest_common_subsequence_table(s, t)
print m + n - (2 * C[m][n])
def main(argv):
s, t = fasta.read_ordered(argv[0])
print strings.count_basic_alignments(s, t) % 134217727