Module protkit.seq.nucleotide_sequence

Implements class NucleotideSequence to represent a nucleotide sequence.

IUPAC base symbols for nucleotide sequences: A A Adenine C C Cytosine G G Guanine T T Thymine U U Uracil

W   A or T          Weak
S   G or C          Strong
R   A or G          Purine
Y   C or T          Pyrimidine
K   G or T          Ketone
M   A or C          Amino

B   C or G or T     Not A
D   A or G or T     Not C
H   A or C or T     Not G
V   A or C or G     Not T

N   A, C, G or T    Any base
-                   Gap

See: https://en.wikipedia.org/wiki/Nucleic_acid_notation

Expand source code 
#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Authors:  Fred Senekal (FS)
# Contact:  fred@silicogenesis.com
# License:  GPLv3

"""
Implements class `NucleotideSequence` to represent a nucleotide sequence.

IUPAC base symbols for nucleotide sequences:
    A   A               Adenine
    C   C               Cytosine
    G   G               Guanine
    T   T               Thymine
    U   U               Uracil

    W   A or T          Weak
    S   G or C          Strong
    R   A or G          Purine
    Y   C or T          Pyrimidine
    K   G or T          Ketone
    M   A or C          Amino

    B   C or G or T     Not A
    D   A or G or T     Not C
    H   A or C or T     Not G
    V   A or C or G     Not T

    N   A, C, G or T    Any base
    -                   Gap

See: https://en.wikipedia.org/wiki/Nucleic_acid_notation
"""

from typing import Optional, List, Union
from protkit.seq.sequence import Sequence


class NucleotideSequence(Sequence):
    def __init__(self,
                 sequence: Union[str, List[str]],
                 description: Optional[str] = None,
                 chain_id: Optional[str] = None
                 ):
        super().__init__(sequence, description, chain_id)

Classes

class NucleotideSequence (sequence: Union[str, List[str]], description: Optional[str] = None, chain_id: Optional[str] = None)

Constructor.

Args

sequence : Union[str, List[str]]
The sequence of residue names.
description : Optional[str]
Optional description associated with the sequence.
chain_id : Optional[str]
Optional chain ID associated with the sequence.

Returns

None

Notes

The sequence can be provided as a string or a list of strings. If provided as a string, the string will be converted to a list of strings.

A sequence can be respresented by a string of single letters, such as "AGILE", or a list of three-letter codes such as ["ALA", "GLY", "ILE", "LEU", "GLU"]. For consistency, the sequence is always represented as a list of codes.

Expand source code 
class NucleotideSequence(Sequence):
    def __init__(self,
                 sequence: Union[str, List[str]],
                 description: Optional[str] = None,
                 chain_id: Optional[str] = None
                 ):
        super().__init__(sequence, description, chain_id)

Ancestors

Inherited members