I want to write a programm that tells you if two given raw video files with 420 colorspace are frame identical. So far i have this:
import os
def checkifduplicate(file, file2, width, height):
bytesPerFrame = int(width * height * 12/8)
n1 = int(os.stat(file).st_size / bytesPerFrame)
n2 = int(os.stat(file2).st_size / bytesPerFrame)
if (n1 != n2):
return 0
with open (file, "rb") as f1:
with open(file2, "rb") as f2:
frameF1 = f1.read(bytesPerFrame)
frameF2 = f2.read(bytesPerFrame)
counter = 1
while frameF1 != b"" and frameF2 != b"" and counter <= n1:
if (frameF1 != frameF2):
return 1
frameF1 = f1.read(bytesPerFrame)
frameF2 = f2.read(bytesPerFrame)
counter += 1
return 2
inputFile1 = "1.raw"
inputFile2 = "2.raw"
n = checkifduplicate(inputFile1,inputFile2,3840,2160)
if (n == 0):
print ("Files contain different amounts of Frames... Ending")
elif (n == 1):
print ("Different Frames")
elif (n == 2):
print ("Identical Stream")
pause = input("Press a Key to End...")
If i use two raw files with different size it works properly.
Also if I use the same raw file twice it return 2 (identical stream)
If I copy one raw file tho and rename it and use those 2 files it returns 1 (different frame)
Related
I am trying to create a script to split the pdf pages for the given page numbers/labels from the pdf, the script are producing the split pdf correctly, but few information are losing, and need to be correct
book mark is losing in the separated pdf, if original pdf contains bookmark
if pdf contains the page labels with Roman and arabic page numbers,
like prelims part start with i, ii, iii, iv ... then again main matter part start with Arabic number 1, 2 ,3... and so on, when passing the value of arabic number for split, it is splitting the prelim part (Roman page number), ie., (start = 5, end = 10 ), but it is splitting from (start = V, End = X)
how to correct the issue in the below script
MWE
import re
import regex
import sys
import os
from iPython.ErrorLog import *
from iPython.LaTeX_QC_validation import *
#from pdfrw import PdfReader, PdfWriter
from PyPDF4 import PdfFileWriter,PdfFileReader
from pdfrw import PdfReader, PdfWriter
from pagelabels import PageLabels, PageLabelScheme
pg_info = open('pageinfo.txt','r')
pgcnt=pg_info.read()
pg_info.close()
print(pgcnt)
pgcnt= re.sub(r'<Misc="([0-9]+)" StartPage="([^">].*)">\s*<Misc="(?:[0-9]+)" EndPage="([^">].*)"/>',r'<Misc="\1" StartPage="\2" EndPage="\3"/>',pgcnt,re.I | re.S| re.M)
print(pgcnt)
pno = []
def value(rno):
r = rno.upper()
if (r == 'I'):
return 1
if (r == 'V'):
return 5
if (r == 'X'):
return 10
if (r == 'L'):
return 50
if (r == 'C'):
return 100
if (r == 'D'):
return 500
if (r == 'M'):
return 1000
return -1
def romanToDecimal(str):
res = 0
i = 0
while (i < len(str)):
# Getting value of symbol s[i]
s1 = value(str[i])
if (i + 1 < len(str)):
# Getting value of symbol s[i + 1]
s2 = value(str[i + 1])
# Comparing both values
if (s1 >= s2):
# Value of current symbol is greater
# or equal to the next symbol
res = res + s1
i = i + 1
else:
# Value of current symbol is greater
# or equal to the next symbol
res = res + s2 - s1
i = i + 2
else:
res = res + s1
i = i + 1
return res
def get_pageInfo(pginfo):
global pno
for m in re.finditer(r'<Misc="([0-9]+)" StartPage="([^">].*)" EndPage="([^">].*)"/>',pginfo,re.I):
Start_page = m.group(2)
End_page = m.group(3)
x = Start_page
y = End_page
numeric_test = x.isnumeric()
if not numeric_test:
Start_page = romanToDecimal(Start_page)
else:
Start_page = int(Start_page)
numeric_test = y.isnumeric()
if not numeric_test:
End_page = romanToDecimal(End_page)
else:
End_page = int(End_page)
print(x, Start_page, y, End_page)
pno.append((Start_page,End_page))
return pno
pgdetails = get_pageInfo(pgcnt)
print(pgdetails)
def pdf_splitter(file,start,end,fcount):
fix_start = start
#we will save new splited pdf as "nameofpdf splitted.pdf"
#example if pdf name is "abc.pdf" then it will be saved as "abc splitted.pdf"
new_file_name = str(fcount)+".pdf"
read_file = PdfFileReader(open(file,"rb")) #read pdf
new_pdf = PdfFileWriter() #create write object
start-=1
try:
with open(new_file_name,"wb") as f:
for i in range(start, end):
new_pdf.addPage(read_file.getPage(i))
new_pdf.write(f)
i+=1
f.close()
print("PDF splitted Successfully")
reader = PdfReader(new_file_name)
labels = PageLabels.from_pdf(reader)
newlabel = PageLabelScheme(startpage=0, # the index of the page of the PDF where the labels will start
style="roman lowercase", # See options in PageLabelScheme.styles()
prefix="",
firstpagenum=fix_start) # number to attribute to the first page of this index
labels.append(newlabel) # Adding our page labels to the existing ones
labels.write(reader)
writer = PdfWriter()
writer.trailer = reader
writer.write(new_file_name)
except Exception as e:
print(e)
x = 0
for i in pgdetails:
x += 1
#pvalaue = i
Start,End = i
pdf_splitter('input.pdf',Start,End,x)
sys.exit()
and the page information file (txt) will contain the below information
<Misc="1" StartPage="i">
<Misc="1" EndPage="ii"/>
<Misc="2" StartPage="ii">
<Misc="2" EndPage="ii"/>
<Misc="3" StartPage="iv">
<Misc="3" EndPage="iv"/>
<Misc="4" StartPage="v">
<Misc="4" EndPage="vi"/>
<Misc="5" StartPage="vii">
<Misc="5" EndPage="xiv"/>
<Misc="6" StartPage="xv">
<Misc="6" EndPage="xv"/>
<Misc="7" StartPage="xvi">
<Misc="7" EndPage="xviii"/>
<Misc="8" StartPage="xix">
<Misc="8" EndPage="xx"/>
Thanks in Advance
I'm currently working on a steagnographic application,
and i'm taking each pixel value and embedding data into it one by one
this sequencial processing is taking a long time to process,
the code:
import config_loader
import numpy as np
from PIL import Image
import encryption
import time
def byte2bin(bytestring):
# print("\n from byte 2 bin\n")
# print(bytestring)
bitstring = bin(int.from_bytes(bytestring, byteorder="big"))
return bitstring[2:]
def insert_data_in_pixel(raw_data, string, ptr, bits=1): # this function takes a pixel's data and then converts it to
# binary and then change the last bit to the secret
color = bin(int(raw_data))[2:]
# old = color # troubleshooting lines
color = color[:len(color) - bits]
color = color + string[ptr: ptr + bits]
# print("original-> ", old,"| |added bits ",string[ptr: ptr+bits],"| |Modified-> ", color) # troubleshooting lines
return np.uint8(int(color, 2))
def insert_length(length, new_img): # inserts length of our secret and the length itself is obfuscated
secret_string_len = '<l>' + str(int(length / 4) + 16) + '<l>' # Added ambiguity
secret_string_len = ''.join(format(_, '08b') for _ in bytearray(str(secret_string_len), encoding='utf-8'))
length = len(secret_string_len)
str_len_ptr = 0
for y in range(length):
x = 0
if str_len_ptr < length:
new_img[x][y][0] = insert_data_in_pixel(new_img[x][y][0], secret_string_len, str_len_ptr, bits=3)
str_len_ptr += 3
if str_len_ptr == length:
break
new_img[x][y][1] = insert_data_in_pixel(new_img[x][y][1], secret_string_len, str_len_ptr, bits=3)
str_len_ptr += 3
if str_len_ptr == length:
break
new_img[x][y][2] = insert_data_in_pixel(new_img[x][y][2], secret_string_len, str_len_ptr, bits=2)
str_len_ptr += 2
if str_len_ptr == length:
break
def secret_Loader(): # loads secret from a file
with open('Message.txt', 'r', encoding='utf-8', errors='ignore') as file:
lines = file.readlines()
message = ''.join(lines)
key = config_loader.read('''data['key']''')
# print(key)
enc_message = encryption.encrypt(message, key)
return enc_message
def insert():
start = time.time()
image_path = config_loader.read('''data['environment']['cover_image']''')
photo = Image.open(image_path).convert('RGB') # just insert the image name here
data = np.asarray(photo).copy()
width, height = photo.size
secret = byte2bin(secret_Loader())
secret_pointer = 0
lensecret = len(secret)
insert_length(lensecret, data)
insertion = time.time()
for x in range(1, height):
for y in range(width):
if lensecret > secret_pointer:
# RED
data[x][y][0] = insert_data_in_pixel(data[x][y][0], secret, secret_pointer, bits=2)
secret_pointer += 2
if lensecret == secret_pointer:
break
# Green
data[x][y][1] = insert_data_in_pixel(data[x][y][1], secret, secret_pointer, bits=2)
secret_pointer += 2
if lensecret == secret_pointer:
break
# Blue
data[x][y][2] = insert_data_in_pixel(data[x][y][2], secret, secret_pointer, bits=1)
secret_pointer += 1
if lensecret == secret_pointer:
break
print("data insertion",time.time()-insertion)
generation = time.time()
# print(data)
data = Image.fromarray(data)
print("image generation in ", time.time()-generation)
# data.show()
_ = time.time()
data = data.save(r'stg.PNG')
print("saving time ", time.time()-_)
print('Exectuted in->', time.time() - start)
if __name__ == '__main__':
insert()
the timings
encryption in 1.0841524600982666
data insertion 9.439783811569214
image generation in 0.039893388748168945
saving time 6.283206939697266
Exectuted in-> 17.11327576637268
I thought about multithreading but that is unreliable as every bit in the data is important and it's position in the sequence is also important.
P.S the data insertion time is for 10000
lines of this
this is a message to test the limit of the program let's check when it breaks and how, also i'm running out of words0
so this isn't bad but if it can be improved how can i achieve it?
Full code: https://paste.pythondiscord.com/kenatayuce.py
I am encountering this error when trying to use LSB Steganography on a GIF:
pix = [value for value in imdata.next()[:3] + # 3 pixels extracted at one time
TypeError: 'int' object is not subscriptable
def modPix(pix, data): # Pixels are modified from 8-bit binary
Link to full code: https://paste.pythondiscord.com/kenatayuce.py
datalist = genData(data)
lendata = len(datalist)
imdata = iter(pix)
for i in range(lendata):
pix = [value for value in imdata.__next__()[:3] + # 3 pixels extracted at one time
imdata.__next__()[:3] +
imdata.__next__()[:3]]
for j in range(0, 8):
if (datalist[i][j] == '0' and pix[j]% 2 != 0): # Pixel value = 1 for odd, 0 for even
pix[j] -= 1
elif (datalist[i][j] == '1' and pix[j] % 2 == 0):
if(pix[j] != 0):
pix[j] -= 1
else:
pix[j] += 1
if (i == lendata - 1): # 8th pixel will state whether to stop or to carry on reading
if (pix[-1] % 2 == 0): # 0 = Keep reading.
if(pix[-1] != 0): # 1 = Stop. Message is over.
pix[-1] -= 1
else:
pix[-1] += 1
else:
if (pix[-1] % 2 != 0):
pix[-1] -= 1
pix = tuple(pix)
yield pix[0:3]
yield pix[3:6]
yield pix[6:9]
This program pulls data out of two .CSV files, which are linked here:
https://drive.google.com/folderview?id=0B1SjPejhqNU-bVkzYlVHM2oxdGs&usp=sharing
It's supposed to look for anything after a comma in each of the two files, but my range logic is somehow wrong. I'm running a traceback error to line 101:
"line 101, in calc_corr: sum_smokers_value = sum_smokers_value + float(s_percent_smokers_data[r][1])
IndexError: list index out of range"
I assume it would do the same for the other times [k][1] shows up.
many thanks in advance if there's a way to fix this.
the program so far is:
# this program opens two files containing data and runs a corralation calculation
import math
def main():
try:
print('does smoking directly lead to lung cancer?')
print('''let's find out, shall we?''''')
print('to do so, this program will find correlation between the instances of smokers, and the number of people with lung cancer.')
percent_smokers, percent_cancer = retrieve_csv()
s_percent_smokers_data, c_percent_cancer_data = read_csv(percent_smokers, percent_cancer)
correlation = calc_corr(s_percent_smokers_data, c_percent_cancer_data,)
print('r_value =', corretation)
except IOError as e:
print(str(e))
print('this program has been cancelled. run it again.')
def retrieve_csv():
num_times_failed = 0
percent_smokers_opened = False
percent_cancer_opened = False
while((not percent_smokers_opened) or (not percent_cancer_opened)) and (num_times_failed < 5):
try:
if not percent_smokers_opened:
percent_smokers_input = input('what is the name of the file containing the percentage of smokers per state?')
percent_smokers = open(percent_smokers_input, 'r')
percent_smokers_opened = True
if not percent_cancer_opened:
percent_cancer_input = input('what is the name of the file containing the number of cases of lung cancer contracted?')
percent_cancer = open(percent_cancer_input, 'r')
percent_cancer_opened = True
except IOError:
print('a file was not located. try again.')
num_times_failed = num_times_failed + 1
if not percent_smokers_opened or not percent_cancer_opened:
raise IOError('you have failed too many times.')
else:
return(percent_smokers, percent_cancer)
def read_csv(percent_smokers, percent_cancer):
s_percent_smokers_data = []
c_percent_cancer_data = []
empty_list = ''
percent_smokers.readline()
percent_cancer.readline()
eof = False
while not eof:
smoker_list = percent_smokers.readline()
cancer_list = percent_cancer.readline()
if smoker_list == empty_list and cancer_list == empty_list:
eof = True
elif smoker_list == empty_list:
raise IOError('smokers file error')
elif cancer_list == empty_list:
raise IOError('cancer file error')
else:
s_percent_smokers_data.append(smoker_list.strip().split(','))
c_percent_cancer_data.append(cancer_list.strip().split(','))
return (s_percent_smokers_data, c_percent_cancer_data)
def calc_corr(s_percent_smokers_data, c_percent_cancer_data):
sum_smokers_value = sum_cancer_cases_values = 0
sum_smokers_sq = sum_cancer_cases_sq = 0
sum_value_porducts = 0
numbers = len(s_percent_smokers_data)
for k in range(0, numbers):
sum_smokers_value = sum_smokers_value + float(s_percent_smokers_data[k][1])
sum_cancer_cases_values = sum_cancer_cases_values + float(c_percent_cancer_data[k][1])
sum_smokers_sq = sum_smokers_sq + float(s_percent_smokers_data[k][1]) ** 2
sum_cancer_cases_sq = sum_cancer_cases_sq + float(c_percent_cancer_data[k][1]) ** 2
sum_value_products = sum_value_products + float(percent_smokers[k][1]) ** float(percent_cancer[k][1])
numerator_value = (numbers * sum_value_products) - (sum_smokers_value * sum_cancer_cases_values)
denominator_value = math.sqrt(abs((numbers * sum_smokers_sq) - (sum_smokers_value ** 2)) * ((numbers * sum_cancer_cases_sq) - (sum_cancer_cases_values ** 2)))
return numerator_value / denominator_value
main()
The values in each row of your data files are not comma separated, but rather tab separated. You need to change the ',' delimiter character you're splitting on for '\t'. Or perhaps use the csv module and tell it that your delimiter is '\t'. You can read more about the csv module in the documentation.
I am working on a program that estimates the statistic Tajima's D in a series of sliding windows across a chromosome. The chromosome itself is also divided into a number of different regions with (hopefully) functional significance. The sliding window analysis is performed by my script on each region.
At the start of the program, I define the size of the sliding windows and the size of the steps that move from one window to the next. I import a file which contains the coordinates for each different chromosomal region, and import another file which contains all the SNP data I am working with (this is read line-by-line, as it is a large file). The program loops through the list of chromosomal locations. For each location, it generates an index of steps and windows for the analysis, partitions the SNP data into output files (corresponding with the steps), calculates key statistics for each step file, and combines these statistics to estimate Tajima's D for each window.
The program works well for small files of SNP data. It also works well for the first iteration over the first chromosomal break point. However, for large files of SNP data, the step size in the analysis is inexplicably decreased as the program iterates over each chromosomal regions. For the first chromosomal regions, the step size is 2500 nucleotides (this is what it is suppose to be). For the second chromosome segment, however, the step size is 1966, and for the third it is 732.
If anyone has any suggestions at to why this might be the case, please let me know. I am especially stumped as this program seems to work size for small files but not for larger ones.
My code is below:
import sys
import math
import fileinput
import shlex
import string
windowSize = int(500)
stepSize = int(250)
n = int(50) #number of individuals in the anaysis
SNP_file = open("SNPs-1.txt",'r')
SNP_file.readline()
breakpoints = open("C:/Users/gwilymh/Desktop/Python/Breakpoint coordinates.txt", 'r')
breakpoints = list(breakpoints)
numSegments = len(breakpoints)
# Open a file to store the Tajima's D results:
outputFile = open("C:/Users/gwilymh/Desktop/Python/Sliding Window Analyses-2/Tajima's D estimates.txt", 'a')
outputFile.write(str("segmentNumber\tchrSegmentName\tsegmentStart\tsegmentStop\twindowNumber\twindowStart\twindowStop\tWindowSize\tnSNPs\tS\tD\n"))
#Calculating parameters a1, a2, b1, b2, c1 and c2
numPairwiseComparisons=n*((n-1)/2)
b1=(n+1)/(3*(n-1))
b2=(2*(n**2+n+3))/(9*n*(n-1))
num=list(range(1,n)) # n-1 values as a list
i=0
a1=0
for i in num:
a1=a1+(1/i)
i=i+1
j=0
a2=0
for j in num:
a2=a2+(1/j**2)
j=j+1
c1=(b1/a1)-(1/a1**2)
c2=(1/(a1**2+a2))*(b2 - ((n+2)/(a1*n))+ (a2/a1**2) )
counter6=0
#For each segment, assign a number and identify the start and stop coodrinates and the segment name
for counter6 in range(counter6,numSegments):
segment = shlex.shlex(breakpoints[counter6],posix = True)
segment.whitespace += '\t'
segment.whitespace_split = True
segment = list(segment)
segmentName = segment[0]
segmentNumber = int(counter6+1)
segmentStartPos = int(segment[1])
segmentStopPos = int(segment[2])
outputFile1 = open((("C:/Users/gwilymh/Desktop/Python/Sliding Window Analyses-2/%s_%s_Count of SNPs and mismatches per step.txt")%(str(segmentNumber),str(segmentName))), 'a')
#Make output files to index the lcoations of each window within each segment
windowFileIndex = open((("C:/Users/gwilymh/Desktop/Python/Sliding Window Analyses-2/%s_%s_windowFileIndex.txt")%(str(segmentNumber),str(segmentName))), 'a')
k = segmentStartPos - 1
windowNumber = 0
while (k+1) <=segmentStopPos:
windowStart = k+1
windowNumber = windowNumber+1
windowStop = k + windowSize
if windowStop > segmentStopPos:
windowStop = segmentStopPos
windowFileIndex.write(("%s\t%s\t%s\n")%(str(windowNumber),str(windowStart),str(windowStop)))
k=k+stepSize
windowFileIndex.close()
# Make output files for each step to export the corresponding SNP data into + an index of these output files
stepFileIndex = open((("C:/Users/gwilymh/Desktop/Python/Sliding Window Analyses-2/%s_%s_stepFileIndex.txt")%(str(segmentNumber),str(segmentName))), 'a')
i = segmentStartPos-1
stepNumber = 0
while (i+1) <= segmentStopPos:
stepStart = i+1
stepNumber = stepNumber+1
stepStop = i+stepSize
if stepStop > segmentStopPos:
stepStop = segmentStopPos
stepFile = open((("C:/Users/gwilymh/Desktop/Python/Sliding Window Analyses-2/%s_%s_step_%s.txt")%(str(segmentNumber),str(segmentName),str(stepNumber))), 'a')
stepFileIndex.write(("%s\t%s\t%s\n")%(str(stepNumber),str(stepStart),str(stepStop)))
i=i+stepSize
stepFile.close()
stepFileIndex.close()
# Open the index file for each step in current chromosomal segment
stepFileIndex = open((("C:/Users/gwilymh/Desktop/Python/Sliding Window Analyses-2/%s_%s_stepFileIndex.txt")%(str(segmentNumber),str(segmentName))), 'r')
stepFileIndex = list(stepFileIndex)
numSteps = len(stepFileIndex)
while 1:
currentSNP = SNP_file.readline()
if not currentSNP: break
currentSNP = shlex.shlex(currentSNP,posix=True)
currentSNP.whitespace += '\t'
currentSNP.whitespace_split = True
currentSNP = list(currentSNP)
SNPlocation = int(currentSNP[0])
if SNPlocation > segmentStopPos:break
stepIndexBin = int(((SNPlocation-segmentStartPos-1)/stepSize)+1)
#print(SNPlocation, stepIndexBin)
writeFile = open((("C:/Users/gwilymh/Desktop/Python/Sliding Window Analyses-2/%s_%s_step_%s.txt")%(str(segmentNumber),str(segmentName),str(stepIndexBin))), 'a')
writeFile.write((("%s\n")%(str(currentSNP[:]))))
writeFile.close()
counter3=0
for counter3 in range(counter3,numSteps):
# open up each step in the list of steps across the chromosomal segment:
L=shlex.shlex(stepFileIndex[counter3],posix=True)
L.whitespace += '\t'
L.whitespace_split = True
L=list(L)
#print(L)
stepNumber = int(L[0])
stepStart = int(L[1])
stepStop = int(L[2])
stepSize = int(stepStop-(stepStart-1))
#Now open the file of SNPs corresponding with the window in question and convert it into a list:
currentStepFile = open(("C:/Users/gwilymh/Desktop/Python/Sliding Window Analyses-2/%s_%s_step_%s.txt")%(str(segmentNumber),str(segmentName),str(counter3+1)),'r')
currentStepFile = list(currentStepFile)
nSNPsInCurrentStepFile = len(currentStepFile)
print("number of SNPs in this step is:", nSNPsInCurrentStepFile)
#print(currentStepFile)
if nSNPsInCurrentStepFile == 0:
mismatchesPerSiteList = [0]
else:
# For each line of the file, estimate the per site parameters relevent to Tajima's D
mismatchesPerSiteList = list()
counter4=0
for counter4 in range(counter4,nSNPsInCurrentStepFile):
CountA=0
CountG=0
CountC=0
CountT=0
x = counter4
lineOfData = currentStepFile[x]
counter5=0
for counter5 in range(0,len(lineOfData)):
if lineOfData[counter5]==("A" or "a"): CountA=CountA+1
elif lineOfData[counter5]==("G" or "g"): CountG=CountG+1
elif lineOfData[counter5]==("C" or "c"): CountC=CountC+1
elif lineOfData[counter5]==("T" or "t"): CountT=CountT+1
else: continue
AxG=CountA*CountG
AxC=CountA*CountC
AxT=CountA*CountT
GxC=CountG*CountC
GxT=CountG*CountT
CxT=CountC*CountT
NumberMismatches = AxG+AxC+AxT+GxC+GxT+CxT
mismatchesPerSiteList=mismatchesPerSiteList+[NumberMismatches]
outputFile1.write(str(("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n")%(segmentNumber, segmentName,stepNumber,stepStart,stepStop,stepSize,nSNPsInCurrentStepFile,sum(mismatchesPerSiteList))))
outputFile1.close()
windowFileIndex = open((("C:/Users/gwilymh/Desktop/Python/Sliding Window Analyses-2/%s_%s_windowFileIndex.txt")%(str(segmentNumber),str(segmentName))), 'r')
windowFileIndex = list(windowFileIndex)
numberOfWindows = len(windowFileIndex)
stepData = open((("C:/Users/gwilymh/Desktop/Python/Sliding Window Analyses-2/%s_%s_Count of SNPs and mismatches per step.txt")%(str(segmentNumber),str(segmentName))), 'r')
stepData = list(stepData)
numberOfSteps = len(stepData)
counter = 0
for counter in range(counter, numberOfWindows):
window = shlex.shlex(windowFileIndex[counter], posix = True)
window.whitespace += "\t"
window.whitespace_split = True
window = list(window)
windowNumber = int(window[0])
firstCoordinateInCurrentWindow = int(window[1])
lastCoordinateInCurrentWindow = int(window[2])
currentWindowSize = lastCoordinateInCurrentWindow - firstCoordinateInCurrentWindow +1
nSNPsInThisWindow = 0
nMismatchesInThisWindow = 0
counter2 = 0
for counter2 in range(counter2,numberOfSteps):
step = shlex.shlex(stepData[counter2], posix=True)
step.whitespace += "\t"
step.whitespace_split = True
step = list(step)
lastCoordinateInCurrentStep = int(step[4])
if lastCoordinateInCurrentStep < firstCoordinateInCurrentWindow: continue
elif lastCoordinateInCurrentStep <= lastCoordinateInCurrentWindow:
nSNPsInThisStep = int(step[6])
nMismatchesInThisStep = int(step[7])
nSNPsInThisWindow = nSNPsInThisWindow + nSNPsInThisStep
nMismatchesInThisWindow = nMismatchesInThisWindow + nMismatchesInThisStep
elif lastCoordinateInCurrentStep > lastCoordinateInCurrentWindow: break
if nSNPsInThisWindow ==0 :
S = 0
D = 0
else:
S = nSNPsInThisWindow/currentWindowSize
pi = nMismatchesInThisWindow/(currentWindowSize*numPairwiseComparisons)
print(nSNPsInThisWindow,nMismatchesInThisWindow,currentWindowSize,S,pi)
D = (pi-(S/a1))/math.sqrt(c1*S + c2*S*(S-1/currentWindowSize))
outputFile.write(str(("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n")%(segmentNumber,segmentName,segmentStartPos,segmentStopPos,windowNumber,firstCoordinateInCurrentWindow,lastCoordinateInCurrentWindow,currentWindowSize,nSNPsInThisWindow,S,D)))
A quick search shows that you do change your stepSize on line 110:
stepStart = int(L[1])
stepStop = int(L[2])
stepSize = int(stepStop-(stepStart-1))
stepStop and stepStart appear to depend on your files' contents, so we can't debug it further.