Files and Sys Module

Reading Files

# ✅ Best way - file automatically closes
with open("data.txt", "r") as file:
    content = file.read()
    print(content)

# ❌ Old way - must manually close (don't do this)
file = open("data.txt", "r")
content = file.read()
file.close()  # Easy to forget!

File Modes

# Read
with open("data.txt", "r") as f:
    content = f.read()

# Write (overwrites!)
with open("output.txt", "w") as f:
    f.write("Hello, World!")

# Append (adds to end)
with open("log.txt", "a") as f:
    f.write("New entry\n")

Reading Methods

read() - Entire File

with open("data.txt") as f:
    content = f.read()  # Whole file as string

readline() - One Line at a Time

with open("data.txt") as f:
    first = f.readline()   # First line
    second = f.readline()  # Second line

readlines() - All Lines as List

with open("data.txt") as f:
    lines = f.readlines()  # ['line1\n', 'line2\n', ...]

Looping Through Files

# Best way - memory efficient
with open("data.txt") as f:
    for line in f:
        print(line, end="")  # Line already has \n

# With line numbers
with open("data.txt") as f:
    for i, line in enumerate(f, start=1):
        print(f"{i}: {line}", end="")

# Strip newlines
with open("data.txt") as f:
    for line in f:
        line = line.strip()  # Remove \n
        print(line)

# Process as list
with open("data.txt") as f:
    lines = [line.strip() for line in f]

Writing Files

write() - Single String

with open("output.txt", "w") as f:
    f.write("Hello\n")
    f.write("World\n")

writelines() - List of Strings

lines = ["Line 1\n", "Line 2\n", "Line 3\n"]
with open("output.txt", "w") as f:
    f.writelines(lines)

print() to File

with open("output.txt", "w") as f:
    print("Hello, World!", file=f)
    print("Another line", file=f)

Processing Lines

Splitting

# By delimiter
line = "name,age,city"
parts = line.split(",")  # ['name', 'age', 'city']

# By whitespace (default)
line = "John   25   NYC"
parts = line.split()  # ['John', '25', 'NYC']

# With max splits
line = "a,b,c,d,e"
parts = line.split(",", 2)  # ['a', 'b', 'c,d,e']

Joining

words = ['Hello', 'World']
sentence = " ".join(words)  # "Hello World"

lines = ['line1', 'line2', 'line3']
content = "\n".join(lines)

Processing CSV Data

with open("data.csv") as f:
    for line in f:
        parts = line.strip().split(",")
        name, age, city = parts
        print(f"{name} is {age} from {city}")

The sys Module

Command Line Arguments

import sys

print(sys.argv)  # List of all arguments
# python script.py hello world
# Output: ['script.py', 'hello', 'world']

print(sys.argv[0])  # Script name
print(sys.argv[1])  # First argument
print(len(sys.argv))  # Number of arguments

Basic Argument Handling

import sys

if len(sys.argv) < 2:
    print("Usage: python script.py <filename>")
    sys.exit(1)

filename = sys.argv[1]
print(f"Processing: {filename}")

Processing Multiple Arguments

import sys

# python script.py file1.txt file2.txt file3.txt
for filename in sys.argv[1:]:  # Skip script name
    print(f"Processing: {filename}")

Argument Validation

import sys
import os

def main():
    # Check argument count
    if len(sys.argv) != 3:
        print("Usage: python script.py <input> <output>")
        sys.exit(1)
    
    input_file = sys.argv[1]
    output_file = sys.argv[2]
    
    # Check if input exists
    if not os.path.exists(input_file):
        print(f"Error: {input_file} not found")
        sys.exit(1)
    
    # Check if output exists
    if os.path.exists(output_file):
        response = input(f"{output_file} exists. Overwrite? (y/n): ")
        if response.lower() != 'y':
            print("Aborted")
            sys.exit(0)
    
    # Process files
    process(input_file, output_file)

if __name__ == "__main__":
    main()

Standard Streams

stdin, stdout, stderr

import sys

# Read from stdin
line = sys.stdin.readline()

# Write to stdout (like print)
sys.stdout.write("Hello\n")

# Write to stderr (for errors)
sys.stderr.write("Error: failed\n")

Reading from Pipe

# In terminal
cat data.txt | python script.py
echo "Hello" | python script.py

# script.py
import sys

for line in sys.stdin:
    print(f"Received: {line.strip()}")

Exit Codes

import sys

# Exit with success
sys.exit(0)

# Exit with error
sys.exit(1)

# Exit with message
sys.exit("Error: something went wrong")

Useful sys Attributes

import sys

# Python version
print(sys.version)         # '3.10.0 (default, ...)'
print(sys.version_info)    # sys.version_info(major=3, ...)

# Platform
print(sys.platform)        # 'linux', 'darwin', 'win32'

# Module search paths
print(sys.path)

# Maximum integer
print(sys.maxsize)

# Default encoding
print(sys.getdefaultencoding())  # 'utf-8'

Building Command Line Tools

Simple Script Template

#!/usr/bin/env python3
"""Simple command line tool."""

import sys
import os

def print_usage():
    print("Usage: python tool.py <input_file>")
    print("Options:")
    print("  -h, --help    Show help")
    print("  -v, --verbose Verbose output")

def main():
    # Parse arguments
    if len(sys.argv) < 2 or sys.argv[1] in ['-h', '--help']:
        print_usage()
        sys.exit(0)
    
    verbose = '-v' in sys.argv or '--verbose' in sys.argv
    
    # Get input file
    input_file = None
    for arg in sys.argv[1:]:
        if not arg.startswith('-'):
            input_file = arg
            break
    
    if not input_file:
        print("Error: No input file", file=sys.stderr)
        sys.exit(1)
    
    if not os.path.exists(input_file):
        print(f"Error: {input_file} not found", file=sys.stderr)
        sys.exit(1)
    
    # Process
    if verbose:
        print(f"Processing {input_file}...")
    
    with open(input_file) as f:
        for line in f:
            print(line.strip())
    
    if verbose:
        print("Done!")

if __name__ == "__main__":
    main()

Word Count Tool

#!/usr/bin/env python3
import sys

def count_file(filename):
    lines = words = chars = 0
    with open(filename) as f:
        for line in f:
            lines += 1
            words += len(line.split())
            chars += len(line)
    return lines, words, chars

def main():
    if len(sys.argv) < 2:
        print("Usage: python wc.py <file1> [file2] ...")
        sys.exit(1)
    
    total_l = total_w = total_c = 0
    
    for filename in sys.argv[1:]:
        try:
            l, w, c = count_file(filename)
            print(f"{l:8} {w:8} {c:8} {filename}")
            total_l += l
            total_w += w
            total_c += c
        except FileNotFoundError:
            print(f"Error: {filename} not found", file=sys.stderr)
    
    if len(sys.argv) > 2:
        print(f"{total_l:8} {total_w:8} {total_c:8} total")

if __name__ == "__main__":
    main()

FASTA Sequence Counter

#!/usr/bin/env python3
import sys

def process_fasta(filename):
    sequences = 0
    total_bases = 0
    
    with open(filename) as f:
        for line in f:
            line = line.strip()
            if line.startswith(">"):
                sequences += 1
            else:
                total_bases += len(line)
    
    return sequences, total_bases

def main():
    if len(sys.argv) != 2:
        print("Usage: python fasta_count.py <file.fasta>")
        sys.exit(1)
    
    filename = sys.argv[1]
    
    try:
        seqs, bases = process_fasta(filename)
        print(f"Sequences: {seqs}")
        print(f"Total bases: {bases}")
        print(f"Average: {bases/seqs:.1f}")
    except FileNotFoundError:
        print(f"Error: {filename} not found", file=sys.stderr)
        sys.exit(1)

if __name__ == "__main__":
    main()

File Path Operations

import os

# Join paths (cross-platform)
path = os.path.join("folder", "subfolder", "file.txt")

# Get filename
os.path.basename("/path/to/file.txt")  # "file.txt"

# Get directory
os.path.dirname("/path/to/file.txt")   # "/path/to"

# Split extension
name, ext = os.path.splitext("data.txt")  # "data", ".txt"

# Check existence
os.path.exists("file.txt")    # True/False
os.path.isfile("file.txt")    # True if file
os.path.isdir("folder")       # True if directory

# Get file size
os.path.getsize("file.txt")   # Size in bytes

# Get absolute path
os.path.abspath("file.txt")

Practice Exercises

Quick Reference

Best Practices

Solution Hints