Lesson 7: Introduction to functions notebook - Introduction to Python For Bioinformatics

def ratio(x, y):
    """The ratio of `x` to `y`."""
    return x / y

def ratio(x, y):
    """The ratio of `x` to `y`.
    return the result"""
    result = x / y
    return result

help(ratio)

Help on function ratio in module __main__:

ratio(x, y)
    The ratio of `x` to `y`.
    return the result

ratio?

?ratio

? ratio

ratio ?

  Cell In[7], line 1
    ratio ?
          ^
SyntaxError: invalid syntax

?ratio

?print

type(ratio)

function

ratio(4 / 2)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[11], line 1
----> 1 ratio(4 / 2)

TypeError: ratio() missing 1 required positional argument: 'y'

ratio(4, 2)

2.0

ratio(4, 2)
print("I hope you liked your result")

I hope you liked your result

def ratio2(x, y):
    """The ratio of `x` to `y`."""
    print(x / y)

ratio(4, 2)

2.0

def ratio(x, y):
    """The ratio of `x` to `y`."""
    return x / y

ratio(4, 2)

2.0

result = ratio(4, 2)
print(result)

2.0

result = ratio2(4, 2)
print(result)

2.0
None

result

ratio(10, 7)

1.4285714285714286

def answer_to_the_ultimate_question_of_life_the_universe_and_everything():
    """Simpler program than Deep Thought's, I bet."""
    return 42

answer_to_the_ultimate_question_of_life_the_universe_and_everything

<function __main__.answer_to_the_ultimate_question_of_life_the_universe_and_everything()>

answer_to_the_ultimate_question_of_life_the_universe_and_everything()

42

ratio

<function __main__.ratio(x, y)>

ratio(5, 3)

1.6666666666666667

answer_to_the_ultimate_question_of_life_the_universe_and_everything()

42

print('Hello world')

Hello world

print()

pi = 3.14159

pi = 22/7

pi

3.142857142857143

def pi():
    return 3.14159

pi()

3.14159

def greet(name):
    print('Hello', name)

result = greet('Jonathan')

Hello Jonathan

result

int = float

int('4')

4.0

int == __builtin__.int

False

int == __builtin__.float

True

int = __builtin__.int

int('4')

4

def int(name):
    print('Hello', name)

int('Peter')

Hello Peter

int = __builtin__.int

def complement_base(base):
    """Returns the Watson-Crick complement of a base."""
    if base in 'Aa':
        return 'T'
    elif base in 'Tt':
        return 'A'
    elif base in 'Gg':
        return 'C'
    elif base in 'Cc':
        return 'G'
    else:
        return 'N'

complement_base('N')

'N'

complement_base('c')

'G'

seq = 'GACAGACTCCATGNNNNNNNCACGTGGGUATCTGTC'

complement_base(seq)

'N'

def complement(seq):
    """Complement an entire sequence of DNA"""
    complement_seq = ''
    for base in seq:
        complement_seq += complement_base(base)
    return complement_seq

complement(seq)

'CTGTCTGAGGTACNNNNNNNGTGCACCCNTAGACAG'

list(reversed(seq))

['C',
 'T',
 'G',
 'T',
 'C',
 'T',
 'A',
 'U',
 'G',
 'G',
 'G',
 'T',
 'G',
 'C',
 'A',
 'C',
 'N',
 'N',
 'N',
 'N',
 'N',
 'N',
 'N',
 'G',
 'T',
 'A',
 'C',
 'C',
 'T',
 'C',
 'A',
 'G',
 'A',
 'C',
 'A',
 'G']

reversed(seq)

<reversed at 0x7fda3860b970>

next(reversed(seq))

'C'

seq[::-1]

'CTGTCTAUGGGTGCACNNNNNNNGTACCTCAGACAG'

def rev_complement(seq):
    """Reverse complement an entire sequence of DNA"""
    complement_seq = ''
    for base in reversed(seq):
        complement_seq += complement_base(base)
    return complement_seq

seq

'GACAGACTCCATGNNNNNNNCACGTGGGUATCTGTC'

rev_complement(seq)

'GACAGATNCCCACGTGNNNNNNNCATGGAGTCTGTC'

seq = 'GATACCA'

rev_complement(seq)

'TGGTATC'

complement_base()

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[63], line 1
----> 1 complement_base()

TypeError: complement_base() missing 1 required positional argument: 'base'

def complement_base(base, moltype='DNA'):
    """Returns the Watson-Crick complement of a base.
    base: str - a single character base
    moltype: str - can be 'DNA' or 'RNA', the type of biomolecule
    """
    print('moltype is', moltype)
    if base in 'Aa':
        if moltype == 'DNA':
            return 'T'
        elif moltype == 'RNA':
            return 'U'
    elif base in 'TtUu':
        return 'A'
    elif base in 'Gg':
        return 'C'
    elif base in 'Cc':
        return 'G'
    else:
        return 'N'

complement_base('U', moltype='RNA')

moltype is RNA

'A'

complement_base('A')

moltype is DNA

'T'

complement_base('A', moltype='DNA')

moltype is DNA

'T'

?print

def greet(*names):
    print("names:", type(names))

greet('Peter')

names: <class 'tuple'>

def greet(*names):
    for name in names:
        print('Hello', name)

greet('Peter')

Hello Peter

greet('Peter', 'Thabo')

Hello Peter
Hello Thabo