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repeatFeatures.py
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import sys
def getComplement(seq):
return seq[::-1]
def getReverse(seq):
comp = getComplement(seq)
comp = comp.replace('a', 'i')
comp = comp.replace('t', 'a')
comp = comp.replace('i', 't')
comp = comp.replace('c', 'i')
comp = comp.replace('g', 'c')
comp = comp.replace('i', 'g')
return comp
def numPalindromes(seq, j):
num_palindromes = 0
current_seq = ''
for i in range(len(seq)):
if i < j:
current_seq += seq[i]
else:
comp_seq = getComplement(current_seq)
if comp_seq == seq[i:i+j] or comp_seq == seq[i+1:i+j+1]:
num_palindromes += 1
current_seq = current_seq[1:] + seq[i]
return num_palindromes
def maxPalindrome(seq):
max_palindrome = 0
for j in range(3, len(seq)/2):
if numPalindromes(seq, j) > 0:
max_palindrome = j
return max_palindrome
def numReverseLocal(seq, j):
num_reverse = 0
current_seq = ''
for i in range(len(seq)/2):
if i < j:
current_seq += seq[i]
else:
rev_seq = getReverse(current_seq)
if rev_seq in seq[i:]:
num_reverse += 1
return num_reverse
current_seq = current_seq[1:] + seq[i]
return num_reverse
def maxReverseLocal(seq):
max_reverse_local = 0
for j in range(7, len(seq)):
if numReverseLocal(seq, j) > 0:
max_reverse_local = j
return max_reverse_local
def numReverseAcross(seq, seq2, j):
num_reverse = 0
current_seq = ''
for i in range(len(seq)):
if i < j:
current_seq += seq[i]
else:
rev_seq = getReverse(current_seq)
if rev_seq in seq2:
num_reverse += 1
return num_reverse
current_seq = current_seq[1:] + seq[i]
return num_reverse
def maxReverseAcross(seq, seq2):
max_reverse_across = 0
for j in range(7, len(seq)):
if numReverseAcross(seq, seq2, j) > 0:
max_reverse_across = j
return max_reverse_across
def numDirectLocal(seq, j):
num_direct = 0
current_seq = ''
for i in range(len(seq)/2):
if i < j:
current_seq += seq[i]
else:
if current_seq in seq[i:]:
num_direct += 1
return num_direct
current_seq = current_seq[1:] + seq[i]
return num_direct
def maxDirectLocal(seq):
max_direct_local = 0
for j in range(7, len(seq)):
if numDirectLocal(seq, j) > 0:
max_direct_local = j
return max_direct_local
def numDirectAcross(seq, seq2, j):
num_direct = 0
current_seq = ''
for i in range(len(seq)):
if i < j:
current_seq += seq[i]
else:
if current_seq in seq2:
num_direct += 1
return num_direct
current_seq = current_seq[1:] + seq[i]
return num_direct
def maxDirectAcross(seq, seq2):
max_direct_across = 0
for j in range(7, len(seq)):
if numDirectAcross(seq, seq2, j) > 0:
max_direct_across = j
return max_direct_across
def AT(seq):
num_a = seq.count('a')
num_t = seq.count('t')
a_t = (num_a + num_t)/15.0
return a_t
def distToIntegrase(start, end, accn, file_name):
mini = 10000000
dist = 0
gff = open(file_name + '.RefSeq.gff', 'r')
for row in gff:
col = row.strip().split('\t')
if col[0] == accn:
if 'integrase' in col[8] or 'recombinase' in col[8]:
if int(col[3]) > start and int(col[3]) < end:
dist1 = abs(start - int(col[3]))
dist2 = abs(end - int(col[4]))
if dist1 < dist2:
dist = dist1
else:
dist = dist2
if dist < mini:
mini = dist
gff.close()
return mini
input = open(sys.argv[1], 'r')
output = open('features', 'w')
prev_fna = ''
dna_seq = {}
for row in input:
columns = row.strip().split('\t')
if columns[0] != prev_fna:
fna = open(columns[0] + '.fna', 'r')
### Read Frags and DNA seqs
current_accn = '<'
current_dna_seq = ''
dna_seq = {}
for r in fna:
r = r.strip()
if len(r) > 0 and r[0] == '>':
dna_seq[current_accn] = current_dna_seq
current_accn = r.split()[0][1:]
current_dna_seq = ''
else:
current_dna_seq += r
dna_seq[current_accn] = current_dna_seq
### Finish reading frags and DNA Seqs ###
fna.close()
prev_fna = columns[0]
accn = columns[1]
start = int(columns[2])
end = int(columns[3])
start_seq = dna_seq[accn][start - 100: start + 115]
end_seq = dna_seq[accn][end - 100: end + 115]
a_t = round(AT(start_seq), 2)
num_palindromes_L = numPalindromes(start_seq, 3)
num_palindromes_R = numPalindromes(end_seq, 3)
max_palindromes_L = maxPalindrome(start_seq)
max_palindromes_R = maxPalindrome(end_seq)
num_direct_local_L = numDirectLocal(start_seq, 7)
num_direct_local_R = numDirectLocal(end_seq, 7)
num_direct_across_L = numDirectAcross(start_seq, end_seq, 7)
num_direct_across_R = numDirectAcross(end_seq, start_seq, 7)
num_reverse_local_L = numReverseLocal(start_seq, 7)
num_reverse_local_R = numReverseLocal(end_seq, 7)
num_reverse_across_L = numReverseAcross(start_seq, end_seq, 7)
num_reverse_across_R = numReverseAcross(end_seq, start_seq, 7)
max_direct_local_L = 0#maxDirectLocal(start_seq)
max_direct_local_R = maxDirectLocal(end_seq)
max_reverse_local_L = 0#maxReverseLocal(start_seq)
max_reverse_local_R = maxReverseLocal(end_seq)
max_direct_across_L = 0#maxDirectAcross(start_seq, end_seq)
max_direct_across_R = maxDirectAcross(end_seq, start_seq)
max_reverse_across_L = 0#maxReverseAcross(start_seq, end_seq)
max_reverse_across_R = maxReverseAcross(end_seq, start_seq)
dist_to_integrase = distToIntegrase(start, end, accn, columns[0])
output.write(str(start) + '\t' + str(end) + '\t' + str(a_t) + '\t' + str(num_palindromes_L) + '\t' + str(num_palindromes_R) + '\t' + str(max_palindromes_L) + '\t' + str(max_palindromes_R) + '\t')
output.write(str(num_direct_local_L) + '\t' + str(num_direct_local_R) + '\t' + str(num_direct_across_L) + '\t' + str(num_direct_across_R) + '\t')
output.write(str(num_reverse_local_L) + '\t' + str(num_reverse_local_R) + '\t' + str(num_reverse_across_L) + '\t' + str(num_reverse_across_R) + '\t')
output.write(str(max_direct_local_R) + '\t' + str(max_reverse_local_R) + '\t')
output.write(str(max_direct_across_R) + '\t' + str(max_reverse_across_R) + '\n') #'\t' + str(dist_to_integrase) + '\n')
output.close()
input.close()