def kmer(): d = {} for x in itertools.product('ACGT', repeat=4): tmp = ''.join(x) d[tmp] = 0 arr = util.read_fasta('rosalind_kmer.txt') dna = arr[0] for i in range(len(dna) - 3): x = dna[i:i+4] d[x] += 1 for x in itertools.product('ACGT', repeat=4): tmp = ''.join(x) print d[tmp],
def main(): arr = util.read_fasta('rosalind_long.txt') result = dna_superstring(arr)
from solutions import util arr = util.read_fasta('rosalind_tran.txt') def main(dna1, dna2): transitions = 0 transversions = 0 for i, x in enumerate(dna1): y = dna2[i] if x != y: if x == 'G' and y == 'A': transitions += 1 elif x == 'A' and y == 'G': transitions += 1 elif x == 'C' and y == 'T': transitions += 1 elif x == 'T' and y == 'C': transitions += 1 else: transversions += 1 return transitions * 1.0 / transversions print main(arr[0], arr[1])
k += 1 return results # assert odd_palindrome('T', 0) == (0, 1) # print odd_palindrome('TTA', 1) # assert odd_palindrome('TTA', 1) == (0, 3) # assert odd_palindrome('CTTAG', 2) == (0, 5) # assert odd_palindrome('TTTAG', 2) == (1, 3) # assert odd_palindrome('ATTATTG', 2) == (0, 5) # assert odd_palindrome('CATTATT', 3) == (1, 5) def revp(input): results = [] for i, x in enumerate(input): even = even_palindrome(input, i) # odd = odd_palindrome(input, i) if even: results += even # if odd: # results += odd for pos, length in results: print pos + 1, length input = 'TCAATGCATGCGGGTCTATATGCAT' arr = util.read_fasta('rosalind_revp.txt') print arr[0] revp(arr[0])
def main(): arr = util.read_fasta('rosalind_motz.txt') print(motz(arr[0]) % 1000000)
def main(): arr = util.read_fasta('rosalind_lcsq.txt') result = lcsq(arr[0], arr[1]) verify(arr[0], result) verify(arr[1], result) print(result)
def main(): arr = util.read_fasta('rosalind_edit.txt') print(edit(arr[0], arr[1]))
def main(): arr = util.read_fasta('rosalind_cat2.txt') print catalan(arr[0]) % 1000000
def main(): arr = util.read_fasta('rosalind_lcsm.txt') return lcsm(arr)
def main(): arr = util.read_fasta('rosalind_kmp.txt') return ' '.join(str(x) for x in failure_arr(arr[0]))
def pdst(): arr = util.read_fasta('rosalind_pdst.txt') n = len(arr) result = [[dist(x, y) for x in arr] for y in arr] for row in result: print ' '.join(map(str, row))
def main(): arr = util.read_fasta('rosalind_corr.txt') corr(arr)
def pmch(): arr = read_fasta('rosalind_pmch.txt') rna = arr[0] counts = Counter(rna) return factorial(counts['U']) * factorial(counts['C'])
def main(): arr = util.read_fasta('rosalind_mmch.txt') rna = arr[0] print mmch(rna)