def main(argv):
line = files.read_line(argv[0])
if palindrome_anagram(line):
print('YES')
else:
print('NO')
def main(argv):
line = files.read_line(argv[0])
perm = [int(val) for val in line[1:-1].split(' ')]
perms = sorts.greedy_reversal_sort(perm)[1]
print '\n'.join('(%s)' % (' '.join('+%s' % p if p > 0 else '%s' % p
for p in perm)) for perm in perms)
def main(argv):
line = files.read_line(argv[0])
handle = ExPASy.get_sprot_raw(line)
record = SwissProt.read(handle)
go = filter(lambda x: x[0] == 'GO' and 'P:' in x[2],
record.cross_references)
print '\n'.join(g[2].split(':')[1] for g in go)
def main(argv):
line = files.read_line(argv[0])
edges = [
tuple(int(node) for node in edge.split(', '))
for edge in line[1:-1].split('), (')
]
genome = genetics.graph_to_genome(edges)
print ''.join('(%s)' % (' '.join('+%s' % p if p > 0 else '%s' % p
for p in g)) for g in genome)
def main(argv):
cypher_text = files.read_line(argv[0])
decrypted = encdec.padding_oracle_decrypt(cypher_text, 'http://crypto-class.appspot.com/po', 'er')
print
print 'Padding Oracle Demo'
print
print 'Found: ', decrypted
print
print ' Hex: ', decrypted.encode('hex')
print
def main(argv):
text = files.read_line(argv[0])
st = tree.SuffixTree(text)
print st.longest_repeat()
sa = arrays.suffix_array(text + '$')
ha = arrays.lcp_array(sa)
index = max(ha, key=lambda x: x[1])
print text[sa[index[0]][0]:sa[index[0]][0] + index[1]]
def main(argv):
S = files.read_line(argv[0])
L = len(S)
D = [int(c) for c in S]
O = D[0]
T = D[0]
for i in range(1, L):
T = (T * 10) + ((i + 1) * D[i])
T %= 1000000007
O += T
O %= 1000000007
print(O)
def main(argv):
S = files.read_line(argv[0])
L = len(S)
D = [int(c) for c in S]
O = D[0]
T = D[0]
for i in range(1, L):
T = (T * 10) + ((i + 1) * D[i])
T %= 1000000007
O += T
O %= 1000000007
print(O)
def main(argv):
line = files.read_line(argv[0])
length = len(line)
orfs = []
sequence = Seq(line, IUPAC.unambiguous_dna)
string = str(sequence)
for pos in re.finditer('ATG', string):
start = pos.start()
end = length - ((length - start) % 3)
orfs.append(translate(string[start:end], to_stop = True))
sequence = sequence.reverse_complement()
string = str(sequence)
for pos in re.finditer('ATG', string):
start = pos.start()
end = length - ((length - start) % 3)
orfs.append(translate(string[start:end], to_stop = True))
print max(orfs, key = len)
def main(argv):
dna = files.read_line(argv[0])
N = len(dna)
sa = arrays.suffix_array(dna)
lcp = arrays.lcp_array(sa)
sub1 = sum(len(sa[i][1][:-1]) - lcp[i][1] for i in xrange(1, N + 1))
st = tree.SuffixTree(dna)
sub2 = sum(len(s) - 1 if s[-1] == '$' else len(s) for s in st.traverse())
m = sum([min(4 ** i, N - i + 1) for i in xrange(N)])
print
print 'suffix tree - lc: %0.4g' % (sub1 / float(m))
print
print 'suffix array - lc: %0.4g' % (sub2 / float(m))
print
def main(argv):
mass = table.mass(argv[0])
protein = files.read_line(argv[1])
print '%0.3f' % genetics.protein_mass(protein, mass)
def main(argv):
if is_pangram(files.read_line(argv[0])):
print('pangram')
else:
print('not pangram')
def main(argv):
print genetics.dna_to_rna(files.read_line(argv[0]))
def main(argv):
text = files.read_line(argv[0])
sa = arrays.suffix_array(text)
print ', '.join(str(v[0]) for v in sa)
def main(argv):
int_mass = table.integer_mass(argv[0])
peptide = files.read_line(argv[1])
masses = [int_mass[p] for p in peptide]
print ' '.join(str(mass) for mass in genetics.cyclo_spectrum(masses))
def main(argv):
codon = table.codon(argv[0])
rna = files.read_line(argv[1])
print genetics.encode_protein(rna, codon)
def main(argv):
text = files.read_line(argv[0])
print(encrypt(text))
def main(argv):
line = files.read_line(argv[0])
tree = genotype_probs(Tree(line, format=1))
print '%0.3g %0.3g %0.3g' % (tree.AA, tree.Aa, tree.aa)
def main(argv):
print(find(files.read_line(argv[0])))
def main(argv):
tree = files.read_line(argv[0])
print '\n'.join(phylogeny.create_table_from_tree(tree))
def main(argv):
text = files.read_line(argv[0])
print strings.inverse_burrows_wheeler_transform(text)
def main(argv):
print genetics.dna_complement(files.read_line(argv[0]))
def main(argv):
print genetics.pattern_to_number(files.read_line(argv[0]))
def main(argv):
line = files.read_line(argv[0])
chromosome = [int(val) for val in line[1:-1].split(' ')]
print '(%s)' % ' '.join(
str(c) for c in genetics.chromosome_to_cycle(chromosome))
def main(argv):
T = files.read_line(argv[0])
print(time_conversion(T))
def main(argv):
line = files.read_line(argv[0])
cycle = [int(val) for val in line[1:-1].split(' ')]
print '(%s)' % ' '.join('+%s' % c if c > 0 else '%s' % c for c in genetics.cycle_to_chromosome(cycle))
def main(argv):
rev_codon = table.reverse_codon(argv[0])
string = files.read_line(argv[1])
print genetics.count_rnas_from_protein(string, rev_codon)
def main(argv):
line = files.read_line(argv[0])
seq = Seq(line)
print seq.count('A'), seq.count('C'), seq.count('G'), seq.count('T')
def main(argv):
line = files.read_line(argv[0])
genome = [[int(val) for val in chromosome.split(' ')]
for chromosome in line[1:-1].split(')(')]
print ', '.join(str(c) for c in genetics.colored_edges_from_genome(genome))
def main(argv):
if is_pangram(files.read_line(argv[0])):
print('pangram')
else:
print('not pangram')
def main(argv):
genome = files.read_line(argv[0])
skew = genetics.reverse_skew_table(genome)
print ' '.join(str(i) for i in skew[min(skew)])
def main(argv):
text = files.read_line(argv[0])
st = tree.SuffixTree(text)
print '\n'.join(st.traverse())
def main(argv):
text = files.read_line(argv[0])
print(encrypt(text))
def main(argv):
line = files.read_line(argv[0])
perm = [int(val) for val in line[1:-1].split(' ')]
print sorts.count_signed_breaks(perm)
def main(argv):
T = files.read_line(argv[0])
print(time_conversion(T))
def main(argv):
print(find(files.read_line(argv[0])))
