*Learn_Errors.md

Major types of errors in Python programming

Syntax Errors, also known as parsing errors

The syntax errors indicate the syntax or structure of the code is incorrect. They are detected by the compiler or the interpreter.

Concatenate 2 different types of objects

print('6 % 6 = ' + 6 % 6)
  Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: can only concatenate str (not "int") to str

Compare a number with a string

age = input('Please type your age: ')
print('Are you older than 10?', age > 10)
Traceback (most recent call last):
File "<pyshell#42>", line 1, in <module>
  print('Are you older than 10?', age > 10)
TypeError: '>' not supported between instances of 'str' and 'int'

Wrongly written keywords

Cell In[17], line 3
return y
^
SyntaxError: 'return' outside function

Name is not defined (e.g., wrong variable/function names)

a = 8
print(AA)
Traceback (most recent call last):
  File "<pyshell#37>", line 1, in <module>
  print(AA)
NameError: name 'AA' is not defined. Did you mean: 'aa'?

NameError                                 Traceback (most recent call last)
Cell In[18], line 1
----> 1 devide_two(98.920)
NameError: name 'devide_two' is not defined

Wrong input

age = int(input('Please type your age: '))
Sixteen
Traceback (most recent call last):
  File "<pyshell#44>", line 1, in <module>
  age = int(input('Please type your age: '))
ValueError: invalid literal for int() with base 10: 'Sixteen'

age = input('Please type your age: ')
try:
    age = int(age)
    print('How old will you be in 2 year?', age + 1)
except ValueError:
    print('The given age is not valid')

Setting extra parameters

TypeError                                 Traceback (most recent call last)
Cell In[14], line 4
2 y = 5
3 # Which of the two variables above has the smallest absolute value?
----> 4 smallest_abs = min(abs(x, y))
TypeError: abs() takes exactly one argument (2 given)

Two starred expressions in assignment

*__, a, b, *_ = ['a', 'cde', 'bib', 6, 9, 10]
File "<stdin>", line 1
SyntaxError: two starred expressions in assignment

Wrong use of an operator

Forgetting parentheses in a function call

Call the locally scoped function

def house():
  print("Gallary from house()")
  def first_house():
      print("Gallary from first_house()")
  def second_house():
      print("Gallary from second_house()")
  first_house()
  second_house()

first_house()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'first_house' is not defined

Not putting strings in single quotes or double quotes

Runtime Errors

No compatible binary

DEBUG [main] Printing verbose output
Traceback (most recent call last):
  File "/Users/your_name/.pyenv/versions/3.8.18/bin/kb", line 8, in <module>
    sys.exit(main())
  File "/Users/your_name/.pyenv/versions/3.8.18/lib/python3.8/site-packages/ngs_tools/logging.py", line 62, in inner
    return func(*args, **kwargs)
  File "/Users/your_name/.pyenv/versions/3.8.18/lib/python3.8/site-packages/kb_python/main.py", line 1583, in main
    raise UnsupportedOSError(
  kb_python.config.UnsupportedOSError: Failed to find compatible kallisto binary. Provide a compatible binary with the --kallisto option or    run kb compile."

No compatible tensor shape

data_1 = torch.tensor([[1, 5, 6], [2, 6, 9]])
data_2 = torch.tensor([[0, 1], [3, 3]])
data_1 + data_2
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
RuntimeError: The size of tensor a (3) must match the size of tensor b (2) at non-singleton dimension 1

Logical Errors

More reading

• https://docs.python.org/3/tutorial/errors.html

Handle errors

Method 1: try-except-else or try-except

Case 1:

def cubic(number): 
    """Returns the cubic of a number."""
    try: 
        return number ** 3
    except:
        print("The number you've input must be an int or float.")
        
cubic('hello')

Case 1.1:

def cubic(number): 
    """Returns the cubic of a number."""
    try: 
        return number ** 3
    except TypeError: # Allow other errors except TypeError pass through
        print("The number you've input must be an int or float.")
        
cubic('hello')

Case 2:

nums = [1, 2, "A"]
sum_nums = 0
for item in nums:
    try:
        float_num = float(item)
    except (ValueError, TypeError) as e:
        print(f"This is a non-numeric item: {item}")
    else:
        sum_nums += float_num 
        print(f"{sum_nums=}")

Case 3: bioinformatics scenarior: load the BAM file and print reads in a specific region

import pysam
try:
    bam_file = pysam.AlignmentFile("alignment.bam", "rb")
except FileNotFoundError:
    print("Error: The BAM file 'alignment.bam' was not found.")
except (IOError, ValueError) as e:
    print(f"Error: An error occurred while reading the BAM file: {e}")
else:
    for read in bam_file.fetch('chr8', 100, 120):
        print(read)
        
    bam_file.close()

Method 2: raise:

def sqrt(number): 
    """Returns the square root of a number."""
    if number < 0:
        raise ValueError("The number you've input must be non-negative.")
    try: 
        return number ** 0.5
    except TypeError:
        print("The number you've input must be an int or float.")
        
sqrt('hello')
sqrt(-8)