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):
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):
pam250 = table.scoring(argv[0])
lines = files.read_lines(argv[1])
result = strings.local_alignment(lines[0], lines[1], pam250)
print result[0]
print '\n'.join(result[1:])
def main(argv):
blosom62 = table.scoring(argv[0])
lines = files.read_lines(argv[1])
result = strings.linear_space_alignment(lines[0], lines[1], blosom62)
print result[0]
print '\n'.join(result[1:])
def main(argv):
blosom62 = table.scoring(argv[0])
s, t = files.read_lines(argv[1])
edge = strings.middle_edge(s, t, blosom62)
print edge[0], edge[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]