def main():
strings = parse_fasta('problem_datasets/rosalind_corr.txt')
strings += [rev_comp(i) for i in strings]
corr = error_correct(strings)
with open('output/rosalind_corr_out.txt', 'w') as outfile:
for i in corr:
outfile.write('->'.join(i) + '\n')
def count_apperances(string_list):
''' Count how many times a given DNA string occurs in a list. If the reverse
complement of that string occurs in the list, it counts towards the
original.
'''
str_count = {}
for i in string_list:
if i in str_count:
str_count[i] += 1
else:
if rev_comp(i) in str_count:
str_count[rev_comp(i)] += 1
else:
str_count[i] = 1
str_count[rev_comp(i)] = 1
return str_count
def locate_sites(f_dna):
r_dna = rev_comp(f_dna)
for i in range(4, 13, 2):
for j in range(len(f_dna)):
f = f_dna[j:j + i]
r = r_dna[len(r_dna) - j - i:len(r_dna) - j]
if f == r:
yield (j + 1, i)
def locate_sites(f_dna):
r_dna = rev_comp(f_dna)
for i in range(4, 13, 2):
for j in range(len(f_dna)):
f = f_dna[j:j+i]
r = r_dna[len(r_dna)-j-i:len(r_dna)-j]
if f == r:
yield j+1, i
def count_apperances(string_list):
''' Count how many times a given DNA string occurs in a list. If the reverse
complement of that string occurs in the list, it counts towards the
original.
'''
str_count = {}
for i in string_list:
if i in str_count:
str_count[i] += 1
else:
if rev_comp(i) in str_count:
str_count[rev_comp(i)] += 1
else:
str_count[i] = 1
str_count[rev_comp(i)] = 1
return str_count
def main():
strings = parse_fasta('problem_datasets/rosalind_corr.txt')
strings += [rev_comp(i) for i in strings]
corr = error_correct(strings)
with open('output/rosalind_corr_out.txt', 'w') as outfile:
for i in corr:
outfile.write('->'.join(i) + '\n')
def raw_translate(seq):
''' Translate all 6 ORFs (3 for the forward strand, 3 for the reverse). '''
table = rosalind_utils.codon_table()
peptides = ['' for x in range(6)]
rev = rosalind_utils.rev_comp(seq)
for i in range(3):
for j in range(i, len(seq), 3):
codon = seq[j:j + 3]
aa = table.get(codon, '-')
peptides[i] += aa
for j in range(i, len(rev), 3):
codon = rev[j:j + 3]
aa = table.get(codon, '-')
peptides[i + 3] += aa
return (peptides)
def raw_translate(seq):
''' Translate all 6 ORFs (3 for the forward strand, 3 for the reverse). '''
table = rosalind_utils.codon_table()
peptides = ['' for x in range(6)]
rev = rosalind_utils.rev_comp(seq)
for i in range(3):
for j in range(i, len(seq), 3):
codon = seq[j:j+3]
aa = table.get(codon,'-')
peptides[i] += aa
for j in range(i, len(rev), 3):
codon = rev[j:j+3]
aa = table.get(codon,'-')
peptides[i+3] += aa
return(peptides)
