Please find details forAssignment 4(Total of 2 data files + PDF with details about the assignment...

Question

Please find details forAssignment 4(Total of 2 data files + PDF with details about the assignment itself). The first file (PDF) details the question/s. Theupstream regions fileis bzipped so you will have to unzip it before using while thecounts matrix is being uploaded as a text file. These files are all in space/tab-delimited text format. As always I am expecting the scripts to be submitted so that when they are run with these files in the current directory with their names as such I have the desired output from your script/program.

Yogesh · Accepted Answer

import math as m
from collections import Counter
def freq_mat_gen(a_cMat, c_cMat, g_cMat, t_cMat, a_fMat, c_fMat, g_fMat, t_fMat):
	
	div_fac = a_cMat[0] + c_cMat[0] + g_cMat[0] + t_cMat[0]
	#print(div_fac)
	
	for i in a_cMat:
		j = i/div_fac
		j = round(j, 3)
		a_fMat.append(j)
	#print(a_fMat)
		
	for i in c_cMat:
		j = i/div_fac
		j = round(j, 3)
		c_fMat.append(j)
	#print(c_fMat)
		
	for i in g_cMat:
		j = i/div_fac
		j = round(j, 3)
		g_fMat.append(j)
	#print(g_fMat)
		
	for i in t_cMat:
		j = i/div_fac
		j = round(j, 3)
		t_fMat.append(j)
	#print(t_fMat)
	
	matrix = []
	matrix.append(a_fMat)
	matrix.append(c_fMat)
	matrix.append(g_fMat)
	matrix.append(t_fMat)
	### For printing the matrix 
	for i in range(4):
		for j in range(18):
			print(matrix[i][j], end = "	")
		print('
')
	print('')
def Freq_Mat_1():
	global a_fMat1, c_fMat1, g_fMat1, t_fMat1
	a_fMat1 = []
	c_fMat1 = []
	g_fMat1 = []
	t_fMat1 = []
	
	print("	Freq. Matrix - F(b, j)")
	freq_mat_gen(a_cMat1, c_cMat1, g_cMat1, t_cMat1, a_fMat1, c_fMat1, g_fMat1, t_fMat1)
	
def pseudocount(a_cMat, c_cMat, g_cMat, t_cMat):
	global a_cMat2, c_cMat2, g_cMat2, t_cMat2
	a_cMat2 = []
	c_cMat2 = []
	g_cMat2 = []
	t_cMat2 = []
	
	for i in a_cMat:
		j = i +1
		a_cMat2.append(j)
		
	for i in c_cMat:
		j = i +1
		c_cMat2.append(j)
		
	for i in g_cMat:
		j = i +1
		g_cMat2.append(j)
		
	for i in t_cMat:
		j = i +1
		t_cMat2.append(j)
		
def Freq_Mat_2():
	global a_fMat2, c_fMat2, g_fMat2,

Please find details forAssignment 4(Total of 2 data files + PDF with details about the assignment itself). The first file (PDF) details the question/s. Theupstream regions fileis bzipped so you will...

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