Bioinfo Lab

Loading......

Password

Important

Please create a new PPT file, document every subsequent step you take with screenshots, save it as a PDF upon completion of all steps, and submit it to the “Weekly Report Assignment” on Moodle by 23:59 this Sunday.

This is an important part of your “General Performance”. Please ensure timely submission!!!

Tips

tab type the first few letters of a file name or command, then press the Tab key. Linux will automatically complete the rest for you.
history You can see all the commands you have run before.
Try help('modules') to see all available standard library modules.
Use pip list to check installed packages.

1. Log into the remote Linux Server

Linux Server:

IP: click

Port: 13579

User Name: dt + Student ID (e.g. dt2023000001)

Password: dt + Student ID + @biuh2025 (e.g. dt2023000001@biuh2025)

2. Understand Libraries, Packages, and Modules

# Create a new script file
cd ~
nano library_concepts.py

# Type the following code:
# Library: A collection focusing on functionality
# Package: A folder containing multiple modules
# Module: A single .py file

# Check Python's standard library path
import sys
print("Standard library location:")
print(sys.path)

# Show how modules are files
import math
print("\nMath module location:")
print(math.__file__)

# Show how packages are directories
import os
print("\nOS package location:")
print(os.__file__)

# Save: Ctrl + O
# Exit: Ctrl + X

# Run the script
python3 library_concepts.py

3. Explore Python’s Built-in Help System

# Enter Python interactive mode
python3

# In interactive mode, type:
# Discover all available standard library modules
help('modules')

# Get help on a specific module
import math
help(math)

# Check math module contents
dir(math)

# Exit interactive mode
exit()

4. Three Ways to Import Modules

# Create a new script file
cd ~
nano import_methods.py

# Type the following code:
# Method 1: Full Import - Get the whole toolbox
import math
print("Full import: 2^5 =", math.pow(2, 5))

# Method 2: Specific Import - Grab just what you need
from random import randint
print("Specific import: Random dice roll:", randint(1, 6))

# Method 3: Alias Import - Make it short
import pandas as pd
data = {'Birds': ['Eagle', 'Penguin'], 'Speed': [320, 8]}
df = pd.DataFrame(data)
print("Alias import:\n", df)

# Mix them up!
from math import sqrt as sq
print("Mixed style: Square root of 121:", sq(121))

# Save: Ctrl + O
# Exit: Ctrl + X

# Run the script
python3 import_methods.py

5. Practice with Standard Library Modules

# Create a new script file
cd ~
nano stdlib_practice.py

# Type the following code:
# Math module
import math
print("Pi is approximately", math.pi)
print("Square root of 16:", math.sqrt(16))

# Datetime module
import datetime
now = datetime.datetime.now()
print("\nCurrent time:", now)
print("Formatted time:", now.strftime("%H:%M:%S"))

# Timedelta calculation
future_date = now + datetime.timedelta(days=3)
print("Date after 3 days:", future_date.date())

# Random module
from random import choice, shuffle
chars = 'ABC123!@'
password = ''.join([choice(chars) for _ in range(8)])
print("\nRandom password:", password)

numbers = [1, 2, 3, 4, 5]
shuffle(numbers)
print("Shuffled numbers:", numbers)

# OS module
import os
my_folder = "test_documents"
if not os.path.exists(my_folder):
    os.makedirs(my_folder)
    print(f"\nCreated folder: {my_folder}")

# Save: Ctrl + O
# Exit: Ctrl + X

# Run the script
python3 stdlib_practice.py

6. Install Third-Party Libraries with pip

# Open terminal (not Python interactive mode)
# Check pip version
pip3 --version

# Install requests library
pip3 install requests

# List installed packages
pip3 list

# Speed up download using mirror (temporary)
pip3 install -i https://pypi.tuna.tsinghua.edu.cn/simple numpy

# Configure permanent mirror
pip3 config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple

# Verify configuration
pip3 config list

# Upgrade a package
pip3 install --upgrade requests

# Install specific version
pip3 install requests==2.31.0

7. Use the requests Library

# Create a new script file
cd ~
nano requests_demo.py

# Type the following code:
import requests

# Simple GET request
response = requests.get("https://www.baidu.com")
print(f"Status Code: {response.status_code}")
print(f"Response Text (first 100 chars): {response.text[:100]}...")

# Real-world weather check
city = "Beijing"
url = f"http://wttr.in/{city}?format=3"
response = requests.get(url)
print(f"\nWeather in {city}: {response.text}")

# Save: Ctrl + O
# Exit: Ctrl + X

# Run the script
python3 requests_demo.py

8. Build a Formal Weather Reporter

# Create a new script file
cd ~
nano weather_reporter.py

# Type the following code:
import requests
import datetime

def get_weather(city):
    """Fetch weather data from wttr.in"""
    url = f"http://wttr.in/{city}?format=%t+%C"
    response = requests.get(url)
    return response.text.strip()

def weather_report(city):
    """Generate time-stamped weather report"""
    # Note: This uses local server time (UTC)
    time_now = datetime.datetime.now().strftime("%H:%M")
    weather = get_weather(city)
    return f"[{time_now}] Weather in {city}: {weather}"

# Test the function
print(weather_report("London"))
print(weather_report("NewYork"))

# Save: Ctrl + O
# Exit: Ctrl + X

# Run the script
python3 weather_reporter.py

# Question: Is there something wrong? How can we fix it? Hint: we are using the Beijing Time.
# Answer: The time shown is server time (UTC), not Beijing time (UTC+8).
# To fix, you would need timezone handling with pytz library.

9. Create a File Backup Helper

# Create a new script file
cd ~
nano backup_helper.py

# Type the following code:
import os
import shutil

def backup_files(src_folder, dst_folder):
    """Copy all .txt files from source to destination"""
    # Create destination folder if it doesn't exist
    if not os.path.exists(dst_folder):
        os.makedirs(dst_folder)
        print(f"Created backup folder: {dst_folder}")
    
    # Check if source folder exists
    if not os.path.exists(src_folder):
        print(f"Error: Source folder '{src_folder}' not found!")
        return
    
    # Copy all .txt files
    for file in os.listdir(src_folder):
        if file.endswith(".txt"):
            src_path = os.path.join(src_folder, file)
            dst_path = os.path.join(dst_folder, file)
            shutil.copy2(src_path, dst_path)
            print(f"Copied: {file}")

# Test the backup function
# First create some test files
os.makedirs("notes", exist_ok=True)
with open("notes/test1.txt", "w") as f:
    f.write("Important notes")
with open("notes/test2.txt", "w") as f:
    f.write("More notes")

# Run backup
backup_files("notes", "backup")

# Save: Ctrl + O
# Exit: Ctrl + X

# Run the script
python3 backup_helper.py

10. Explore Library Documentation

# Create a new script file
cd ~
nano explore_docs.py

# Type the following code:
# Standard library documentation
import webbrowser

# Open Python standard library docs
webbrowser.open("https://docs.python.org/3/library")

# Open PyPI for third-party libraries
webbrowser.open("https://pypi.org")

# Save: Ctrl + O
# Exit: Ctrl + X

# Run the script
python3 explore_docs.py

# Pro Tip: Great programmers stand on the shoulders of giants
# Always explore documentation before reinventing the wheel

End