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08_Python_files

The document provides an overview of Python files, modules, and packages, explaining their definitions and how to import them. It includes instructions on creating custom modules, running scripts from the command line, using argparse for command-line argument parsing, and working with files for reading and writing data. Additionally, it contains exercises for practical application of the concepts discussed.

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Abdul Basir
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3 views

08_Python_files

The document provides an overview of Python files, modules, and packages, explaining their definitions and how to import them. It includes instructions on creating custom modules, running scripts from the command line, using argparse for command-line argument parsing, and working with files for reading and writing data. Additionally, it contains exercises for practical application of the concepts discussed.

Uploaded by

Abdul Basir
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Python Files and modules

Petr Svarny, 2020


Module, package, library
● There is no strict classification
● Module is file or folder containing code
○ E.g. text file with .py ending
● Package is usually set of several modules
● Library is general name for package, used in other languages also
Module import
● Import whole module using import module, call function as
module.function()

>>> import os
>>> os.getcwd()
'/home/me'

● Import only one function from module import function


>>> from os import getcwd
>>> getcwd()
'/home/me'
Module import
● Using abbreviation import module as mod, call function as mod.function

>>> import pandas as pd


>>> pd.read_table('apple.txt')

● Load module from package as import mod.submodule as mod

>>> import matplotlib.pyplot as plt


>>> plt.plot(x, y)
Module import error
>>> import Bio

---------------------------------------------

ImportError Traceback (most recent call last)

<ipython-input-1-a7440e1156be> in <module>()

----> 1 import Bio

ImportError: No module named 'Bio'


Import module
>>> from datetime import datetime

>>> now_time = datetime.now()

datetime datetime now

Library Object Method


Modules
● Standard library
○ Already installed
○ E.g.: math, os, sys, random
○ More info: https://docs.python.org/3.6/library/
● Other modules
○ Install using pip
■ sudo pip3 install module_name
■ sudo pip install module_name
■ E.g.: pandas, numpy, matplotlib, plotly
Create your own module
Note: module must be in the same directory, or in directory above

hello.py

def print_hello():
print('Hello!')

main_program.py

import hello
hello.print_hello()
Create your own module
If module is in

/home/me/my_modules/hello.py

def print_hello():
print('Hello!')

/home/me/my_scripts/main_program.py

import sys
sys.path.append('/home/me/my_module/')
import hello
hello.print_hello()
Exercise
● Create python file that will contain function divide_two_numbers
● Import this function to a different Python file, main.py, or Jupyter Notebook
● Call function in the second file main.py or in your Jupyter Notebook, e.g.
divide_two_numbers(3,5)
Run python script from command line
Create my_script.py (e.g. in text editor).

$ cat my_script.py

print("Hello world!")

Run script using python3

$ python3 my_script.py

Hello world!
Run python script from command line
● Use sys.argv from sys package
● sys.argv is the list of command-line arguments,
the program name is first argument, i.e. sys.argv[0]

import sys
def sum_num(a,b):
return a+b

print(sum_num(int( sys.argv[1]),int(sys.argv[2])))

$ python my_script.py 3 2
5
Argparse
- Library for parsing arguments from the command-line
- Allows easy help integration
- Use of positional or optional arguments
- See the documentation
Argparse import and start
Argparse positional arguments
Argparse positional arguments with help
Argparse positional arguments with type
Argparse optional arguments
Argparse optional arguments with actions
Argparse optional arguments with short options
Argparse combining arguments
Argparse combining arguments and defaults
Exercise
Write a small Python script count_letters.py using argparse that:

- Has a positional argument of the string in which letters are supposed to be


counted.
- Has two optional arguments:
- v: to count only vowels
- c: count only consonants

The script prints out a list of letters in alphabetical order with the number of
occurrences:

a2

b5
Script structure
Often the script contains a function called “main” just to be clear what is the
purpose of the script. This is, however, not necessary.

On the other hand, the following block can be used to make sure the script’s code
runs only in case the script is directly called:

if __name__ == ’__main__’:

<body that is meant to run>


Exercise
● Write script
● Input values: two strings as arguments from command line
● Script will print number of occurrences of substring in string
● Example:

$python count_occurrence.py ab abcdabcc


String ab occurred 2 times in string abcdabcc.
Exercise
● Write script
● Input values: two strings (word and letter) as arguments from command line
● Script will print word without specified letter
● Example:

$python extract_letter.py python o


pythn

$python extract_letter.py python l


python
Working with files - open
● The same process as we work with the file
○ Open file -> Action (read, write, edit) -> Close file
● open function will create file object
○ open(filename including path, mode)
● open has several modes (can be combined)
○ 'r'- file is opened for reading, error if file does not exist
○ 'r+' - file is opened for reading and writing, error if file does not exist
○ 'w' - file is opened for writing, existing file will have zero length, if file does not exist, new file will
be created
○ 'a' - file is opened for appending at the end of file, if file does not exist, new file will be created
○ 'b' - file will be open in binary mode, e.g. photos, movies.
Working with files - close
● To close file use close method
○ file.close()
● Do not forget to close file, lead to file truncation!
● Solution: use with statement
○ File will close automatically after with statement

>>> f = open('data.txt', 'r+', encoding='utf-8')


>>> data = f.read()
>>> f.close()

>>> with open('data.txt' , 'r+', encoding='utf-8') as f:


... data = f.read()
Working with files - write
● Use write method
>>> with open('hello.txt' , 'w', encoding='utf-8') as f:
... print(type(f))
... f.write('Hello world!' )

>>> fruits = [ 'apple', 'pear', 'apricot', 'banana', 'kiwi']

>>> with open('fruits.txt' , 'w', encoding='utf-8') as f:


... for fruit in fruits:
... f.write(fruit + '\n')
Working with files - read
● Several functions are available
○ read read the whole file as one string
○ readlines read the whole file as list of lists
○ readline read one line and return string

>>> with open('fruits.txt' , 'r', encoding='utf-8') as f:


... fruit_data = f.read()
>>> fruit_data
'apple\npear\napricot\nbanana\nkiwi\n'
Working with files - read
>>> with open('fruit.txt' , 'r', encoding='utf-8') as f:
... fruit_data = f.readlines()
>>> fruit_data
['apples\n', 'apricots\n', 'peaches\n', 'bananas\n']

>>> with open('fruit.txt' , 'r', encoding='utf-8') as f:


... fruit_data = f.readline()
>>> fruit_data
'apples\n'
Working with files - read
>>> with open('fruits.txt' , 'r', encoding='utf-8') as f:
... fruit_data = f.read().splitlines()

>>> fruit_data
['apples', 'apricots', 'peaches', 'bananas']
Offtopic: timing functions in Jupyter Notebook
● Use Jupyter notebook magic function %%timeit or %%time
● More information here
Exercise
● Create list of things you would like to take on the empty island
● Write this list to the tab-delimited file, so that each element is on a different line and lines are
numbered
● Example

1 casserole
2 book
3 knife
4 water bottle
5 fishing rod

● Hint: you can use print with additional parameters

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