Python: Classes and Object-Oriented Design

Python supports object-oriented programming via classes. Objects are instances of classes, and they can possess both data (known as attributes) and class-specific functions (known as methods). Classes can therefore be used to model real world structures that have properties and behaviors.

Self

Class methods have a special first parameter, traditionally called self, that refers to the instance itself. Basically, when we have an instance of a class, say a = A(), and we call an instance method, a.func(x, y, z), the Python interpreter executes A.func(a, x, y, z). Hence there is an extra first argument that is a placeholder i.e., self, referring to the instance calling the method. Examples below will make this concept clearer.

Everything in Python is a class

Even a number is a class

We can show all the attributes and methods with the built-in dir function. Notice that there are special attributes that begin and end with double underscores, and regular ones that do not. We will learn more about special methods later.

', '.join(dir(2))

'__abs__, __add__, __and__, __bool__, __ceil__, __class__, __delattr__, __dir__, __divmod__, __doc__, __eq__, __float__, __floor__, __floordiv__, __format__, __ge__, __getattribute__, __getnewargs__, __gt__, __hash__, __index__, __init__, __init_subclass__, __int__, __invert__, __le__, __lshift__, __lt__, __mod__, __mul__, __ne__, __neg__, __new__, __or__, __pos__, __pow__, __radd__, __rand__, __rdivmod__, __reduce__, __reduce_ex__, __repr__, __rfloordiv__, __rlshift__, __rmod__, __rmul__, __ror__, __round__, __rpow__, __rrshift__, __rshift__, __rsub__, __rtruediv__, __rxor__, __setattr__, __sizeof__, __str__, __sub__, __subclasshook__, __truediv__, __trunc__, __xor__, bit_length, conjugate, denominator, from_bytes, imag, numerator, real, to_bytes'

Define a class

class A:
    """Describe class."""
    pass

Create an instance of the class

a = A()

print(a)

<__main__.A object at 0x104999710>

Special and regular methods

class B:
    """Describe the class."""
    def __init__(self, val):
        """Class initizlizer."""
        self.val = val

    def __str__(self):
        """String reprresntation of class instance."""
        return "{}: {}".format(self.__class__.__name__, self.val)

    def add(self, val):
        """Add val to self.val"""
        self.val += val

This uses the __init__ special method

b = B('hello')

This uses the __str__ special method

print(b)

B: hello

This uses the `add` regular method.

b.add(' world')

print(b)

B: hello world

Inheritance

class C(B):
    def __init__(self, val, name='C'):
        super().__init__(val)
        self.name = name

    def __str__(self):
        """String reprresntation of class instance."""
        return "{}: {}".format(self.name, self.val)

This uses the __init__ method of C. Note that assignment of val is delegated to the parent class.

c = C('hello', 'Rumpelstiltskin')

This uses the add regular method of B, since C has no add method defined.

c.add(' Rapunzel')

This uses the __str__ special method of C, not B.

print(c)

Rumpelstiltskin: hello Rapunzel

Extended Example

We will design a class to store and manipulate biological sequence data. This class has fairly rich functionality using some advanced Python features even though it consists of only a few lines of code.

from collections.abc import Mapping

class BioSequence(Mapping):
    """A class that contains one or more biological sequences."""

    def __init__(self, fasta):
        """Construcror from a FASTA format string."""
        chunks = [x for x in fasta.strip().split('>') if x]
        names = []
        seqs = []
        for chunk in chunks:
            lines = chunk.splitlines()
            names.append(lines[0].strip())
            seqs.append(''.join(lines[1:]))
        self._data = dict(zip(names, seqs))

    def __getitem__(self, key):
        return self._data[key]

    def __iter__(self):
        return iter(self._data)

    def __len__(self):
        return len(self._data)

    def __str__(self):
        return str(self._data)

short = ['Ala', 'Arg', 'Asn', 'Asp', 'Cys', 'Glu', 'Gln',
     'Gly', 'His', 'Ile', 'Leu', 'Lys', 'Met', 'Phe',
     'Pro', 'Ser', 'Thr', 'Trp', 'Tyr', 'Val',
     'ANY', 'GAP', 'STP']

letters = ['A', 'R', 'N', 'D', 'C', 'E', 'Q', 'G', 'H',
           'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W',
           'Y', 'V', 'X', '-', '*']

class PeptideSequence(BioSequence):
    """Specialized class for peptide seequences."""

    def __init__(self, fasta):
        super().__init__(fasta)
        self.mapper = dict(zip(letters, short))

    def __str__(self):
        s = []
        for k, v in self._data.items():
            s.append(k)
            s.append('-'.join(self.mapper[c] for c in v))
            s.append('')
        return '\n'.join(s)

class DNASequence(BioSequence):
    """Specialized class for DNA seequences."""

    def __init__(self, fasta):
        super().__init__(fasta)
        self.table = str.maketrans('ACTG', 'TGAC')

    def reverse_complement(self):
        return {k: v.translate(self.table)[::-1] for
             k, v in self._data.items()}

Creating a class instance for a peptide sequence

peptide_fasta = '''>MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
DIDGDGQVNYEEFVQMMTAK*

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY'''

peptides = PeptideSequence(peptide_fasta)

len(peptides)

2

list(peptides.keys())

['MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken',
 'gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]']

peptides['MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken']

'ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK*'

for k, v in peptides.items():
    print(k, v)
    print()

MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK*

gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY

print(peptides)

MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
Ala-Asp-Gln-Leu-Thr-Glu-Glu-Gln-Ile-Ala-Glu-Phe-Lys-Glu-Ala-Phe-Ser-Leu-Phe-Asp-Lys-Asp-Gly-Asp-Gly-Thr-Ile-Thr-Thr-Lys-Glu-Leu-Gly-Thr-Val-Met-Arg-Ser-Leu-Gly-Gln-Asn-Pro-Thr-Glu-Ala-Glu-Leu-Gln-Asp-Met-Ile-Asn-Glu-Val-Asp-Ala-Asp-Gly-Asn-Gly-Thr-Ile-Asp-Phe-Pro-Glu-Phe-Leu-Thr-Met-Met-Ala-Arg-Lys-Met-Lys-Asp-Thr-Asp-Ser-Glu-Glu-Glu-Ile-Arg-Glu-Ala-Phe-Arg-Val-Phe-Asp-Lys-Asp-Gly-Asn-Gly-Tyr-Ile-Ser-Ala-Ala-Glu-Leu-Arg-His-Val-Met-Thr-Asn-Leu-Gly-Glu-Lys-Leu-Thr-Asp-Glu-Glu-Val-Asp-Glu-Met-Ile-Arg-Glu-Ala-Asp-Ile-Asp-Gly-Asp-Gly-Gln-Val-Asn-Tyr-Glu-Glu-Phe-Val-Gln-Met-Met-Thr-Ala-Lys-STP

gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
Leu-Cys-Leu-Tyr-Thr-His-Ile-Gly-Arg-Asn-Ile-Tyr-Tyr-Gly-Ser-Tyr-Leu-Tyr-Ser-Glu-Thr-Trp-Asn-Thr-Gly-Ile-Met-Leu-Leu-Leu-Ile-Thr-Met-Ala-Thr-Ala-Phe-Met-Gly-Tyr-Val-Leu-Pro-Trp-Gly-Gln-Met-Ser-Phe-Trp-Gly-Ala-Thr-Val-Ile-Thr-Asn-Leu-Phe-Ser-Ala-Ile-Pro-Tyr-Ile-Gly-Thr-Asn-Leu-Val-Glu-Trp-Ile-Trp-Gly-Gly-Phe-Ser-Val-Asp-Lys-Ala-Thr-Leu-Asn-Arg-Phe-Phe-Ala-Phe-His-Phe-Ile-Leu-Pro-Phe-Thr-Met-Val-Ala-Leu-Ala-Gly-Val-His-Leu-Thr-Phe-Leu-His-Glu-Thr-Gly-Ser-Asn-Asn-Pro-Leu-Gly-Leu-Thr-Ser-Asp-Ser-Asp-Lys-Ile-Pro-Phe-His-Pro-Tyr-Tyr-Thr-Ile-Lys-Asp-Phe-Leu-Gly-Leu-Leu-Ile-Leu-Ile-Leu-Leu-Leu-Leu-Leu-Leu-Ala-Leu-Leu-Ser-Pro-Asp-Met-Leu-Gly-Asp-Pro-Asp-Asn-His-Met-Pro-Ala-Asp-Pro-Leu-Asn-Thr-Pro-Leu-His-Ile-Lys-Pro-Glu-Trp-Tyr-Phe-Leu-Phe-Ala-Tyr-Ala-Ile-Leu-Arg-Ser-Val-Pro-Asn-Lys-Leu-Gly-Gly-Val-Leu-Ala-Leu-Phe-Leu-Ser-Ile-Val-Ile-Leu-Gly-Leu-Met-Pro-Phe-Leu-His-Thr-Ser-Lys-His-Arg-Ser-Met-Met-Leu-Arg-Pro-Leu-Ser-Gln-Ala-Leu-Phe-Trp-Thr-Leu-Thr-Met-Asp-Leu-Leu-Thr-Leu-Thr-Trp-Ile-Gly-Ser-Gln-Pro-Val-Glu-Tyr-Pro-Tyr-Thr-Ile-Ile-Gly-Gln-Met-Ala-Ser-Ile-Leu-Tyr-Phe-Ser-Ile-Ile-Leu-Ala-Phe-Leu-Pro-Ile-Ala-Gly-ANY-Ile-Glu-Asn-Tyr

Creating a class instance for a DNA sequence

dna_fasta ='''
>SRR001666_1.
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGA

>SRR001666_2
AAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA
AGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT
'''

dnas = DNASequence(dna_fasta)

print(dnas)

{'SRR001666_1.': 'GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCGTTCAGGGATACGACGTTTGTATTTTAAGAATCTGA', 'SRR001666_2': 'AAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT'}

dnas.reverse_complement()

{'SRR001666_1.': 'TCAGATTCTTAAAATACAAACGTCGTATCCCTGAACGGTGGGATTTGACGCCATCGGCAGCGGCCATCACCC',
 'SRR001666_2': 'ATGATAAAACGACGCGTATTATCATCGACTTCTGCTTCTATTTGAAAACCCTTAAGTTGTTAAGGGTAACTT'}