Module protkit.seq.sequence
Implements class Sequence to represent a sequence of residues.
This class provides a representation of a sequence. The class provides core functionality for sequence alignment and comparison, that is applicable to both nucleotide and protein sequences.
Specific functionality for nucleotide and protein sequences are provided by the NucleotideSequence and ProteinSequence classes.
This class should be able to handle sequences of any length, and of any type (nucleotide or protein). The underlying representation of the sequence should be able to handle any type of sequence.
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#!/usr/bin/env python3
# -*- coding:utf-8 -*-
# Authors: Fred Senekal (FS)
# Contact: fred@silicogenesis.com
# License: GPLv3
"""
Implements class `Sequence` to represent a sequence of residues.
This class provides a representation of a sequence. The class
provides core functionality for sequence alignment and comparison,
that is applicable to both nucleotide and protein sequences.
Specific functionality for nucleotide and protein sequences are
provided by the NucleotideSequence and ProteinSequence classes.
This class should be able to handle sequences of any length, and
of any type (nucleotide or protein). The underlying representation
of the sequence should be able to handle any type of sequence.
"""
from typing import Optional, List, Union
from protkit.core.extend_attributes import ExtendedAttributes
class Sequence(ExtendedAttributes):
def __init__(self,
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.
"""
super().__init__()
if type(sequence) is str:
# Convert string representations to a list representation.
sequence = list(sequence)
self._sequence = sequence
self._chain_id = chain_id
self._description = description
def __str__(self):
"""
Returns a string representation of the sequence.
Returns:
str: The string representation of the sequence.
"""
if self._sequence is None:
return ""
if len(self.sequence) == 0:
return ""
if len(self._sequence[0]) == 1:
spacer = ""
else:
spacer = " "
return spacer.join(self._sequence)
def to_string(self, start_index: int, end_index: int) -> str:
"""
Returns a string representation of a subsequence.
Args:
start_index (int): The start index of the subsequence.
end_index (int): The end index of the subsequence.
Returns:
str: The string representation of the subsequence.
"""
if self._sequence is None or len(self.sequence) == 0:
return ""
sub_sequence = [self._sequence[i] for i in range(start_index, min(end_index + 1, self.length))]
if len(self._sequence[0]) == 1:
return "".join(sub_sequence)
else:
return " ".join(sub_sequence)
def __len__(self):
"""
Returns the length of the sequence.
Returns:
int: The length of the sequence.
"""
return len(self._sequence)
def __getitem__(self, index):
"""
Returns the residue at the specified index.
Args:
index (int): The index of the residue to return.
Returns:
str: The residue at the specified index.
"""
return self._sequence[index]
def __setitem__(self, index, value):
"""
Sets the residue at the specified index.
Args:
index (int): The index of the residue to set.
value (str): The residue to set.
Returns:
None
"""
self._sequence[index] = value
@property
def sequence(self):
"""
Returns the sequence.
Returns:
str: The sequence.
"""
return self._sequence
@sequence.setter
def sequence(self, sequence: Union[str, List[str]]):
"""
Sets the sequence.
Args:
sequence (Union[str, List[str]]): The sequence.
Returns:
None
"""
if type(sequence) is str:
# Convert string representations to a list representation.
self._sequence = list(sequence)
else:
self._sequence = sequence
@property
def description(self):
"""
Returns the description.
Returns:
str: The description.
"""
return self._description
@description.setter
def description(self, description):
"""
Sets the description.
Args:
description (str): The description.
Returns:
None
"""
self._description = description
@property
def chain_id(self):
"""
Returns the chain ID.
Returns:
str: The chain ID.
"""
return self._chain_id
@chain_id.setter
def chain_id(self, chain_id):
"""
Sets the chain ID.
Args:
chain_id (str): The chain ID.
Returns:
None
"""
self._chain_id = chain_id
@property
def length(self):
"""
Returns the length of the sequence.
Returns:
int: The length of the sequence.
"""
return len(self._sequence)Classes
class Sequence (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 Sequence(ExtendedAttributes): def __init__(self, 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. """ super().__init__() if type(sequence) is str: # Convert string representations to a list representation. sequence = list(sequence) self._sequence = sequence self._chain_id = chain_id self._description = description def __str__(self): """ Returns a string representation of the sequence. Returns: str: The string representation of the sequence. """ if self._sequence is None: return "" if len(self.sequence) == 0: return "" if len(self._sequence[0]) == 1: spacer = "" else: spacer = " " return spacer.join(self._sequence) def to_string(self, start_index: int, end_index: int) -> str: """ Returns a string representation of a subsequence. Args: start_index (int): The start index of the subsequence. end_index (int): The end index of the subsequence. Returns: str: The string representation of the subsequence. """ if self._sequence is None or len(self.sequence) == 0: return "" sub_sequence = [self._sequence[i] for i in range(start_index, min(end_index + 1, self.length))] if len(self._sequence[0]) == 1: return "".join(sub_sequence) else: return " ".join(sub_sequence) def __len__(self): """ Returns the length of the sequence. Returns: int: The length of the sequence. """ return len(self._sequence) def __getitem__(self, index): """ Returns the residue at the specified index. Args: index (int): The index of the residue to return. Returns: str: The residue at the specified index. """ return self._sequence[index] def __setitem__(self, index, value): """ Sets the residue at the specified index. Args: index (int): The index of the residue to set. value (str): The residue to set. Returns: None """ self._sequence[index] = value @property def sequence(self): """ Returns the sequence. Returns: str: The sequence. """ return self._sequence @sequence.setter def sequence(self, sequence: Union[str, List[str]]): """ Sets the sequence. Args: sequence (Union[str, List[str]]): The sequence. Returns: None """ if type(sequence) is str: # Convert string representations to a list representation. self._sequence = list(sequence) else: self._sequence = sequence @property def description(self): """ Returns the description. Returns: str: The description. """ return self._description @description.setter def description(self, description): """ Sets the description. Args: description (str): The description. Returns: None """ self._description = description @property def chain_id(self): """ Returns the chain ID. Returns: str: The chain ID. """ return self._chain_id @chain_id.setter def chain_id(self, chain_id): """ Sets the chain ID. Args: chain_id (str): The chain ID. Returns: None """ self._chain_id = chain_id @property def length(self): """ Returns the length of the sequence. Returns: int: The length of the sequence. """ return len(self._sequence)Ancestors
Subclasses
Instance variables
var chain_id-
Returns the chain ID.
Returns
str- The chain ID.
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@property def chain_id(self): """ Returns the chain ID. Returns: str: The chain ID. """ return self._chain_id var description-
Returns the description.
Returns
str- The description.
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@property def description(self): """ Returns the description. Returns: str: The description. """ return self._description var length-
Returns the length of the sequence.
Returns
int- The length of the sequence.
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@property def length(self): """ Returns the length of the sequence. Returns: int: The length of the sequence. """ return len(self._sequence) var sequence-
Returns the sequence.
Returns
str- The sequence.
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@property def sequence(self): """ Returns the sequence. Returns: str: The sequence. """ return self._sequence
Methods
def to_string(self, start_index: int, end_index: int) ‑> str-
Returns a string representation of a subsequence.
Args
start_index:int- The start index of the subsequence.
end_index:int- The end index of the subsequence.
Returns
str- The string representation of the subsequence.
Expand source code
def to_string(self, start_index: int, end_index: int) -> str: """ Returns a string representation of a subsequence. Args: start_index (int): The start index of the subsequence. end_index (int): The end index of the subsequence. Returns: str: The string representation of the subsequence. """ if self._sequence is None or len(self.sequence) == 0: return "" sub_sequence = [self._sequence[i] for i in range(start_index, min(end_index + 1, self.length))] if len(self._sequence[0]) == 1: return "".join(sub_sequence) else: return " ".join(sub_sequence)
Inherited members