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"""Sequence container used throughout ConKit"""
from __future__ import division
from __future__ import print_function
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "0.13.3"
from Bio import pairwise2
from conkit.core.entity import Entity
from conkit.core.mappings import AminoAcidMapping, AminoAcidOneToThree
[docs]class Sequence(Entity):
"""A sequence template to store all associated information
Examples
--------
>>> from conkit.core import Sequence
>>> sequence_entry = Sequence("example", "ABCDEF")
>>> print(sequence_entry)
Sequence(id="example" seq="ABCDEF" seqlen=6)
Attributes
----------
id : str
A unique identifier
remark : list
The :obj:`~conkit.core.sequence.Sequence`-specific remarks
seq : str
The protein sequence as :obj:`str`
seq_len : int
The protein sequence length
"""
__slots__ = ["_remark", "_seq"]
def __init__(self, id, seq):
"""Initialise a generic sequence
Parameters
----------
id : str
A unique sequence identifier
seq : str
The protein sequence
"""
self._remark = []
self._seq = None
self.seq = seq
super(Sequence, self).__init__(id)
def __add__(self, other):
"""Concatenate two sequence instances to a new"""
return Sequence("_".join([self.id, other.id]), self.seq + other.seq)
def __len__(self):
"""The sequence length"""
return len(self._seq)
def __repr__(self):
if self.seq_len > 12:
seq_string = "".join([self.seq[:5], "...", self.seq[-5:]])
else:
seq_string = self.seq
return '{}(id="{}" seq="{}" seq_len={})'.format(self.__class__.__name__, self.id, seq_string, self.seq_len)
@property
def remark(self):
"""The :obj:`~conkit.core.sequence.Sequence`-specific remarks"""
return self._remark
@remark.setter
def remark(self, remark):
"""Set the :obj:`~conkit.core.sequence.Sequence` remark
Parameters
----------
remark : str, list
The remark will be added to the list of remarks
"""
self._remark += Entity.listify(remark)
@property
def seq(self):
"""The protein sequence as :obj:`str`"""
return self._seq
@seq.setter
def seq(self, seq):
"""Set the sequence
Parameters
----------
seq : str
Raises
------
:exc:`ValueError`
One or more amino acids in the sequence are not recognised
"""
if all(AminoAcidOneToThree[c].value for c in seq.upper() if c != "-"):
self._seq = seq
else:
raise ValueError("Unrecognized amino acids in sequence")
@property
def seq_ascii(self):
"""The protein sequence as ASCII-encoded :obj:`str`"""
return bytearray(self._seq, "ascii")
@property
def seq_encoded(self):
"""The protein sequence encoded by numbers"""
return [getattr(AminoAcidMapping, c, AminoAcidMapping.X).value for c in self.seq]
@property
def seq_len(self):
"""The protein sequence length"""
return len(self)
[docs] def align_global(self, other, id_chars=2, nonid_chars=1, gap_open_pen=-0.5, gap_ext_pen=-0.1, inplace=False):
"""Generate a global alignment between two :obj:`~conkit.core.sequence.Sequence` instances
Parameters
----------
other : :obj:`~conkit.core.sequence.Sequence`
id_chars : int, optional
nonid_chars : int, optional
gap_open_pen : float, optional
gap_ext_pen : float, optional
inplace : bool, optional
Replace the saved order of residues [default: False]
Returns
-------
tuple
Tuple containing two :obj:`~conkit.core.sequence.Sequence` instances, regardless of inplace
"""
sequence1 = self._inplace(inplace)
sequence2 = other._inplace(inplace)
alignment = pairwise2.align.globalms(
sequence1.seq, sequence2.seq, id_chars, nonid_chars, gap_open_pen, gap_ext_pen
)
sequence1.seq = alignment[-1][0]
sequence2.seq = alignment[-1][1]
return sequence1, sequence2
[docs] def align_local(self, other, id_chars=2, nonid_chars=1, gap_open_pen=-0.5, gap_ext_pen=-0.1, inplace=False):
"""Generate a local alignment between two :obj:`~conkit.core.sequence.Sequence` instances
Parameters
----------
other : :obj:`~conkit.core.sequence.Sequence`
id_chars : int, optional
nonid_chars : int, optional
gap_open_pen : float, optional
gap_ext_pen : float, optional
inplace : bool, optional
Replace the saved order of residues [default: False]
Returns
-------
tuple
Tuple containing two :obj:`~conkit.core.sequence.Sequence` instances, regardless of inplace
"""
sequence1 = self._inplace(inplace)
sequence2 = other._inplace(inplace)
alignment = pairwise2.align.localms(
sequence1.seq, sequence2.seq, id_chars, nonid_chars, gap_open_pen, gap_ext_pen
)
sequence1.seq = alignment[-1][0]
sequence2.seq = alignment[-1][1]
return sequence1, sequence2
