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 + '$') ha = arrays.lcp_array(sa) index = max(ha, key=lambda x: x[1]) print text[sa[index[0]][0]:sa[index[0]][0] + index[1]]
def main(argv): S = files.read_line(argv[0]) L = len(S) D = [int(c) for c in S] O = D[0] T = D[0] for i in range(1, L): T = (T * 10) + ((i + 1) * D[i]) T %= 1000000007 O += T O %= 1000000007 print(O)
def main(argv): line = files.read_line(argv[0]) length = len(line) orfs = [] sequence = Seq(line, IUPAC.unambiguous_dna) string = str(sequence) for pos in re.finditer('ATG', string): start = pos.start() end = length - ((length - start) % 3) orfs.append(translate(string[start:end], to_stop = True)) sequence = sequence.reverse_complement() string = str(sequence) for pos in re.finditer('ATG', string): start = pos.start() end = length - ((length - start) % 3) orfs.append(translate(string[start:end], to_stop = True)) print max(orfs, key = len)
def main(argv): dna = files.read_line(argv[0]) N = len(dna) sa = arrays.suffix_array(dna) lcp = arrays.lcp_array(sa) sub1 = sum(len(sa[i][1][:-1]) - lcp[i][1] for i in xrange(1, N + 1)) st = tree.SuffixTree(dna) sub2 = sum(len(s) - 1 if s[-1] == '$' 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): 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): line = files.read_line(argv[0]) perm = [int(val) for val in line[1:-1].split(' ')] print sorts.count_signed_breaks(perm)