def main(fname):
seqs, _ = fasta.read(util.find_file(fname))
print "s:", seqs[0]
print "t:", seqs[1]
align, os, ot = edit_distance_alignment(seqs[0], seqs[1])
print align
print os
print ot
def main(fname):
seqs, _ = fasta.read(util.find_file(fname))
corrections = find_corrections(seqs)
for c in corrections:
print c
def main(fname):
seqs, _ = fasta.read(util.find_file(fname))
lcs = find_longest_common_subsequence(seqs[0], seqs[1])
print lcs
def main(fname):
seqs, _ = fasta.read(util.find_file(fname))
print count_matchings(seqs[0])
def run_test(self, sample_name, expected_name):
seqs, _ = fasta.read(util.find_file(sample_name, __file__))
expected = seqio.read_list(util.find_file(expected_name, __file__))
actual = main.find_corrections(seqs)
self.assertItemsEqual(actual, expected)
def main(fname):
seqs, _ = fasta.read(util.find_file(fname))
if len(seqs[0]) != len(seqs[1]):
print "Sequences have different lengths!"
sys.exit(1)
print compute_ratio(seqs[0], seqs[1])
def main(fname):
seqs, _ = fasta.read(util.find_file(fname))
pos = find_subseqs(seqs[0], seqs[1])
print " ".join(map(str, pos))
def main(fname):
seq, _ = fasta.read(util.find_file(fname))
T = build_table(seq[0])
print " ".join(map(str, T))
def main(fname):
seqs, _ = fasta.read(util.find_file(fname))
print(find_shortest_superstring(seqs))
def main(fname):
seqs, _ = fasta.read(util.find_file(fname))
print calc_matches(seqs[0])
def main(fname):
seqs, _ = fasta.read(util.find_file(fname))
result = count_kmers(seqs[0], 4)
print " ".join(map(str, result))
def main(fname):
seqs, _ = fasta.read(util.find_file(fname))
ed = find_edit_distance(seqs[0], seqs[1])
print ed