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Nanopore-tools/Plotting/TraceExtractor.py
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TraceExtractor.py
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### Extracts a part of the trace:
from sys import platform as sys_pf
if sys_pf == 'darwin':
import matplotlib
matplotlib.use("TkAgg")
import os
import numpy as np
import math
import LoadData
#rc('text', usetex=True)
from tkinter import Tk
from tkinter.filedialog import askopenfilenames
root = Tk()
root.withdraw()
filenames = askopenfilenames()
root.update()
for i,file in enumerate(filenames):
dat = LoadData.OpenFile(file)
Data = LoadData.OpenFile(file)
samplerate = Data['samplerate']
trace = Data['i1']
x = np.fromfile(file, np.dtype('>f4'))
f = open(file, 'rb') #rb : Opens the file as read-only in binary format and starts reading from the beginning of the file.
for i in range(10): #range() function. To loop through a set of code a specified number of times, we can use the range() function, The range() function returns a sequence of numbers, starting from 0 by default, and increments by 1 (by default), and ends at a specified number.
a = str(f.readline())
print(a)
end = len(x)
i1 = np.array(x[250:end-1:2])
v1 = np.array(x[251:end:2])
savename2 = 'multiple_trappings_extracted_.dat'
#Save options
os.chdir(os.path.dirname(file))
directory = (str(os.path.split(file)[0]) + os.sep + 'Extracted' + '_traces')
if not os.path.exists(directory):
os.makedirs(directory)
def round_up_to_even(f):
return math.ceil(f / 2.) * 2
startT = round_up_to_even (int(134.2*samplerate)*2) #Specify starting time stamp
endT = round_up_to_even (int(260*samplerate)*2) #Specify ending time stamp
print(startT)
print(endT)
header = x[:250]
data = x[startT:endT]
f2 = open(savename2,'wb') # wb indicates that the file is opened for writing only in binary mode
header.tofile(f2)
data.tofile(f2)
f2.close()
f = open(file, 'rb') # Opens a file for reading only in binary format
f2 = open(savename2,'rb')
for i in range(11):
print(" Lines:")
a = f.readline()
a2 = f2.readline()
print(str(a))
print( " hahaha ")
print(str(a2))
f2.close()
f.close()
print('Done')
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