Lakshmi KrishnaKumaar -4 years ago 91
Python Question

# Using chaos game representation for gene sequences [Python program]

I need to represent many gene sequences using chaos game representation I got this python code from BoĊĦtjan Cigan's blog (https://bostjan-cigan.com/chaos-game-representation-of-gene-structure-in-python/)

# https://bostjan-cigan.com

``````    import collections
from collections import OrderedDict
from matplotlib import pyplot as plt
from matplotlib import cm

import pylab
import math

f = open("ensemblSeq.fa")
data = "".join(s1.split("\n")[1:])

def count_kmers(sequence, k):
d = collections.defaultdict(int)
for i in xrange(len(data)-(k-1)):
d[sequence[i:i+k]] +=1
for key in d.keys():
if "N" in key:
del d[key]
return d

def probabilities(kmer_count, k):
probabilities = collections.defaultdict(float)
N = len(data)
for key, value in kmer_count.items():
probabilities[key] = float(value) / (N - k + 1)
return probabilities

def chaos_game_representation(probabilities, k):
array_size = int(math.sqrt(4**k))
chaos = []
for i in range(array_size):
chaos.append([0]*array_size)

maxx = array_size
maxy = array_size
posx = 1
posy = 1
for key, value in probabilities.items():
for char in key:
if char == "T":
posx += maxx / 2
elif char == "C":
posy += maxy / 2
elif char == "G":
posx += maxx / 2
posy += maxy / 2
maxx = maxx / 2
maxy /= 2
chaos[posy-1][posx-1] = value
maxx = array_size
maxy = array_size
posx = 1
posy = 1

return chaos

f3 = count_kmers(data, 3)
f4 = count_kmers(data, 4)

f3_prob = probabilities(f3, 3)
f4_prob = probabilities(f4, 4)

chaos_k3 = chaos_game_representation(f3_prob, 3)
pylab.title('Chaos game representation for 3-mers')
pylab.imshow(chaos_k3, interpolation='nearest', cmap=cm.gray_r)
pylab.show()

chaos_k4 = chaos_game_representation(f4_prob, 4)
pylab.title('Chaos game representation for 4-mers')
pylab.imshow(chaos_k4, interpolation='nearest', cmap=cm.gray_r)
pylab.show()
``````

This code works fine but I have many sequence files I need to iterate through each fasta file in the folder and get individual plots stored in a folder with the name of the image file corresponding to the name of the fasta file how can I modify the code according to my need

I am new to python as well as StackOverflow if any mistake is there kindly ignore

So, if you want to apply your code on every file in your directory a very simple way to do this is calling all files inside of a `for`-loop. I suggest the following:

``````import collections
import os
from collections import OrderedDict
from matplotlib import pyplot as plt
from matplotlib import cm

import pylab
import math

def count_kmers(sequence, k):
d = collections.defaultdict(int)
for i in xrange(len(data)-(k-1)):
d[sequence[i:i+k]] +=1
for key in d.keys():
if "N" in key:
del d[key]
return d

def probabilities(kmer_count, k):
probabilities = collections.defaultdict(float)
N = len(data)
for key, value in kmer_count.items():
probabilities[key] = float(value) / (N - k + 1)
return probabilities

def chaos_game_representation(probabilities, k):
array_size = int(math.sqrt(4**k))
chaos = []
for i in range(array_size):
chaos.append([0]*array_size)

maxx = array_size
maxy = array_size
posx = 1
posy = 1
for key, value in probabilities.items():
for char in key:
if char == "T":
posx += maxx / 2
elif char == "C":
posy += maxy / 2
elif char == "G":
posx += maxx / 2
posy += maxy / 2
maxx = maxx / 2
maxy /= 2
chaos[posy-1][posx-1] = value
maxx = array_size
maxy = array_size
posx = 1
posy = 1
return chaos

if __name__ == "__main__":
PATH = os.getcwd()
filelist = sorted([os.path.join(PATH, f) for f in os.listdir(PATH) if f.endswith('.fa')])
for file in filelist:
f = open(file)
data = "".join(s1.split("\n")[1:])
f3 = count_kmers(data, 3)
f4 = count_kmers(data, 4)

f3_prob = probabilities(f3, 3)
f4_prob = probabilities(f4, 4)

chaos_k3 = chaos_game_representation(f3_prob, 3)
pylab.title('Chaos game representation for 3-mers')
pylab.imshow(chaos_k3, interpolation='nearest', cmap=cm.gray_r)
pylab.savefig(os.path.splitext(file)[0]+'chaos3.png')
pylab.show()

chaos_k4 = chaos_game_representation(f4_prob, 4)
pylab.title('Chaos game representation for 4-mers')
pylab.imshow(chaos_k4, interpolation='nearest', cmap=cm.gray_r)
pylab.savefig(os.path.splitext(file)[0]+'chaos4.png')
pylab.show()
``````

I just wrapped a loop around and added a `pylab.savefig()` call. Furthermore I used `os` to get the filenames from your directory. It should work now.

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