def resampling_f(fastadict, seq, n, k):
fastadict[seq] = fastadict[seq].replace("N", "").replace("n", "")
seq_list = np.random.choice(tuple(fastadict[seq]),
replace=True,
size=(n * k, )).view('S{k}'.format(k=k))
l = []
for element in seq_list:
new_seq_het = list(
heterozygosity(element))[2] # Het of the new sequence
l.append(new_seq_het)
return l
return intergenicDict
intergenDict = intergenicCoord(intergenic)
if winSize == 0 and step == 0:
# Do not use sliding window approach, just calculate heterozygosity in the given region
new_fastdict = {}
for scaffold in intergenDict.keys():
if scaffold in fastaDict.keys():
for coordinate in intergenDict.get(scaffold):
intron = fastaDict.get(
scaffold)[int(coordinate[0]):int(coordinate[1])]
print(scaffold + '\t' + str(coordinate[0]) + '\t' +
str(coordinate[1]) + '\t' +
str(heterozygosity(intron)[0]) + '\t' +
str(heterozygosity(intron)[1]) + '\t' +
str(heterozygosity(intron)[2]))
# Get a sequence in fasta that lies within the intergenic sequence -- V2
else:
# Print header
print("Scaffold" + "\t" + "Orientation" + "\t" + "Window" + "\t" +
"Window_Start" + "\t" + "Window_End" + "\t" + "Distance_from_Gene" +
"\t" + "Intergenic_start" + "\t" + "Intergenic_end" + "\t" +
"Num_SNPs" + "\t" + "Num_bases" + "\t" + "Het")
new_fastdict = {}
for scaffold in intergenDict.keys():
counter = 0
if scaffold in fastaDict.keys():
# print scaffold
#!/usr/bin/python
from __future__ import division
import sys
from fasta import readfasta
from het import heterozygosity
fasta = sys.argv[1]
# Read fasta into a dictionary
with open(fasta, 'r') as f:
fasta_dict = readfasta(f)
# Calculate heterozygosity for every scaffold
for key in fasta_dict.keys():
het = heterozygosity(fasta_dict[key])
print(key + "\t" + str(het[0]) + "\t" + str(het[1]) + "\t" + str(het[2]))
#**********************************************
intron_dict = {}
for line in intron_coord:
line = line.strip('\n').split('\t')
key, value = line[0], line[1:]
if key in intron_dict.keys():
intron_dict[key].append(value)
else:
intron_dict[key] = [value]
#**************************************************************************
# Extract the intronic sequences from fasta and read them into a dictionary
#**************************************************************************
for scaf in intron_dict.keys():
scaffold = scaf.split('_', 1)[0]
if scaffold in fastaseq.keys():
for coordinate in intron_dict.get(scaf):
# If the sequence is ABCD and the coordinates are 1 and 3, because the
# indexing is from 0 in Python, we would take the sequence from 0 to 3
# because the last base is exclusive.
intron_seq = fastaseq.get(
scaffold)[int(coordinate[0]):int(coordinate[1])]
print(scaf + '\t' + str(coordinate[0]) + '\t' +
str(coordinate[1]) + '\t' +
str(heterozygosity(intron_seq)[0]) + '\t' +
str(heterozygosity(intron_seq)[1]) + '\t' +
str(heterozygosity(intron_seq)[2]))
intron_coord.close()
fasta.close()
for coordinate in intergenDict.get(scaffold):
counter = 0
new_scaffold = fastaDict.get(
scaffold)[int(coordinate[0]):int(coordinate[1]) + 1]
length = len(new_scaffold)
if length % 2 == 1:
length = length + 1
midpoint = int(length / 2)
sequence_left = new_scaffold[0:midpoint]
sequence_right = new_scaffold[:(midpoint - 1):-1]
chunks_left = slidingWindow(sequence_left, winSize, step)
for i in chunks_left:
counter += 1
end = str(int(coordinate[0]) + int(counter * winSize))
start = str(int(end) - winSize)
distance = str(abs(int(coordinate[0]) - int(end)))
print scaffold, "left", counter, start, end, distance, coordinate[
0], coordinate[1], heterozygosity(i)
counter = 0
chunks_right = slidingWindow(sequence_right, winSize, step)
for i in chunks_right:
counter += 1
end = str(int(coordinate[1]) - int(counter * winSize))
start = str(int(end) + winSize)
distance = str(int(coordinate[1]) - int(end))
print scaffold, "right", counter, start, end, distance, coordinate[
0], coordinate[1], heterozygosity(i)
fastaseq.close()
intergenic.close()
with open(window, 'r') as windowfile:
for line in windowfile:
line = line.strip('\n').split('\t')
key, value = line[0], line[1:]
if key in window_dict.keys():
window_dict[key].append(value)
else:
window_dict[key] = [value]
# print window_dict
fasta_win = {}
for scaffold in window_dict.keys():
for element in window_dict.get(scaffold):
if scaffold in fasta_win.keys():
fasta_win[scaffold].append(fasta_dict[scaffold][int(element[0]) -
1:int(element[1])])
else:
fasta_win[scaffold] = [
fasta_dict[scaffold][int(element[0]) - 1:int(element[1])]
]
# print fasta_win
for scaffold in fasta_win.keys():
for sequence in fasta_win.get(scaffold):
index = fasta_win[scaffold].index(sequence)
print scaffold, window_dict[scaffold][index][0], window_dict[scaffold][
index][1], window_dict[scaffold][index][2], heterozygosity(
sequence)[0], heterozygosity(sequence)[1], heterozygosity(
sequence)[2]