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)
