Sequences | Python Fiddle

import itertools

bases = ['A','C','G','T']
complements = {'A':'T','T':'A','C':'G','G':'C'}

# n = length of sequences required
n = 6
# k = length of complementary region on which to exclude sequences
k = 4

# find all sequences of length n
nmers = []
for p in itertools.product(bases,repeat=n):
    nmers.append(''.join(p))
print "Total number of nmers: ",len(nmers)

# remove those with runs of 4 of the same base
no_repeats = []
to_remove = []
if n > 3:
    for sequence in nmers:
    	for i in range(0,n-3):
            if sequence[i] == sequence[i+1] == sequence[i+2] == sequence[i+3]:
                to_remove.append(sequence)
        if not (sequence in to_remove):
            no_repeats.append(sequence)
else:
    no_repeats = nmers
print "Nmers with no runs of 4 identical bases: ",len(no_repeats)

# remove complementary palindromes
no_palindromes = []
for sequence in no_repeats:
    if n % 2 == 0:
        first_half = sequence[:(n/2)]
        second_half = sequence[(n/2):]
    elif n % 2 == 1:
        first_half = sequence[:((n-1)/2)]
        second_half = sequence[((n+1)/2):]
    second_half_reversed = second_half[::-1]
    second_half_rc = []  
    for i in range(0,len(second_half_reversed)):
    	second_half_rc.append(complements[second_half_reversed[i]])
    second_half_rc = ''.join(second_half_rc)
    if first_half != second_half_rc:
            no_palindromes.append(sequence)
print "Nmers excluding palindromes: ",len(no_palindromes)

# remove those which are complementary to chosen sequences

# dictionary of all kmers within each sequence
forward_kmers = {}
for sequence in no_palindromes:
    kmers = []
    for i in range(0,n-k+1):
        kmer = sequence[i:i+k]
        if not (kmer in kmers):
        	kmers.append(sequence[i:i+k])
	forward_kmers[sequence] = kmers

# dictionary of reverse complements of all kmers within each sequence
reverse_kmers = {}
for sequence in forward_kmers:
    all_reverse_complements = []
    for kmer in forward_kmers[sequence]:
        reverse = kmer[::-1]
        reverse_complement = []
        for i in range(0,len(reverse)):
            reverse_complement.append(complements[reverse[i]])
        reverse_complement = ''.join(reverse_complement)
        if not (reverse_complement in all_reverse_complements):
        	all_reverse_complements.append(reverse_complement)
    reverse_kmers[sequence] = all_reverse_complements
   
    
no_complements = []
to_remove = []
m = len(no_palindromes)
for i in range(0,m-1):
    for j in range(i+1,m):
        if set(forward_kmers[no_palindromes[i]]) & set(reverse_kmers[no_palindromes[j]]):
            to_remove.append(no_palindromes[j])

for i in range(0,m):
    if not (no_palindromes[i] in to_remove):
        no_complements.append(no_palindromes[i])
print len(no_complements)

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