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[pull] master from biopython:master #46

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Jan 17, 2025
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[pull] master from biopython:master #46

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163 changes: 1 addition & 162 deletions Bio/motifs/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,6 @@

from Bio import BiopythonDeprecationWarning
from Bio.Align import Alignment
from Bio.Seq import reverse_complement, reverse_complement_rna


def create(instances, alphabet="ACGT"):
Expand Down Expand Up @@ -187,163 +186,14 @@ def read(handle, fmt, strict=True):
return motif


class Instances(list):
"""Class containing a list of sequences that made the motifs."""

def __init__(self, instances=None, alphabet="ACGT"):
"""Initialize the class."""
from Bio.Seq import MutableSeq
from Bio.Seq import Seq

warnings.warn(
"The Instances class has been deprecated; please use the\n"
"Alignment class in Bio.Align instead.\n"
"To create a Motif instance, instead of"
"\n"
">>> from Bio.motifs import Instances\n"
">>> instances = Instances([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')])\n"
">>> motif = Motif(alphabet='ACGT', instances=instances)\n"
"\n"
"please use\n"
"\n"
">>> from Bio.Align import Alignment\n"
">>> alignment = Alignment([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')])\n"
">>> motif = Motif(alphabet='ACGT', alignment=alignment)\n",
BiopythonDeprecationWarning,
)
if isinstance(instances, (Seq, MutableSeq, str)):
raise TypeError(
"instances should be iterator of Seq objects or strings. "
"If a single sequence is given, will treat each character "
"as a separate sequence."
)

length = None
if instances is not None:
sequences = []
for instance in instances:
if length is None:
length = len(instance)
elif length != len(instance):
message = (
"All instances should have the same length (%d found, %d expected)"
% (len(instance), length)
)
raise ValueError(message)
if not isinstance(instance, Seq):
instance = Seq(str(instance))
sequences.append(instance)
# no errors were raised; store the instances:
self.extend(sequences)
self.length = length
self.alphabet = alphabet

def __str__(self):
"""Return a string containing the sequences of the motif."""
text = ""
for instance in self:
text += str(instance) + "\n"
return text

def count(self):
"""Count nucleotides in a position."""
counts = {}
for letter in self.alphabet:
counts[letter] = [0] * self.length
for instance in self:
for position, letter in enumerate(instance):
counts[letter][position] += 1
return counts

def search(self, sequence):
"""Find positions of motifs in a given sequence.

This is a generator function, returning found positions of motif
instances in a given sequence.
"""
warnings.warn(
"""instances.search(sequence) has been deprecated. Please use sequence.search(instances) instead, where sequence is a Seq object.""",
BiopythonDeprecationWarning,
)
for pos in range(len(sequence) - self.length + 1):
for instance in self:
if instance == sequence[pos : pos + self.length]:
yield (pos, instance)
break # no other instance will fit (we don't want to return multiple hits)

def reverse_complement(self):
"""Compute reverse complement of sequences."""
from Bio.Seq import MutableSeq
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

instances = Instances(alphabet=self.alphabet)
instances.length = self.length
if sorted(self.alphabet) == ["A", "C", "G", "T"]:
for instance in self:
if isinstance(instance, (Seq, MutableSeq, SeqRecord)):
instance = instance.reverse_complement()
elif isinstance(instance, str):
instance = reverse_complement(instance)
else:
raise RuntimeError(
"instance has unexpected type %s" % type(instance)
)
instances.append(instance)
elif sorted(self.alphabet) == ["A", "C", "G", "U"]:
for instance in self:
if isinstance(instance, (Seq, MutableSeq, SeqRecord)):
instance = instance.reverse_complement_rna()
elif isinstance(instance, str):
instance = reverse_complement_rna(instance)
else:
raise RuntimeError(
"instance has unexpected type %s" % type(instance)
)
instances.append(instance)
else:
raise ValueError(
"Calculating reverse complement only works for DNA and RNA instances"
)
return instances


class Motif:
"""A class representing sequence motifs."""

def __init__(self, alphabet="ACGT", alignment=None, counts=None, instances=None):
def __init__(self, alphabet="ACGT", alignment=None, counts=None):
"""Initialize the class."""
from . import matrix

self.name = ""
if instances is not None and alignment is not None:
raise Exception(
ValueError, "Specify either alignment or instances, don't specify both"
)
if isinstance(alignment, Instances):
instances = alignment
alignment = None
if instances is not None:
warnings.warn(
"The instances argument has been deprecated.\n"
"Instead of"
"\n"
">>> instances = [Seq('ACGT'), Seq('ACCT'), Seq('AAGT')]\n"
">>> motif = Motif(alphabet='ACGT', instances=instances)\n"
"\n"
"please use\n"
"\n"
">>> from Bio.Align import Alignment\n"
">>> alignment = Alignment([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')])\n"
">>> motif = Motif(alphabet='ACGT', alignment=alignment)\n",
BiopythonDeprecationWarning,
)
if counts is not None:
raise Exception(
ValueError, "Specify either counts or instances, don't specify both"
)
alignment = Alignment(instances)
alphabet = instances.alphabet
if counts is not None and alignment is not None:
raise Exception(
ValueError, "Specify either counts or an alignment, don't specify both"
Expand Down Expand Up @@ -494,17 +344,6 @@ def pssm(self):
"""Calculate and return the position specific scoring matrix for this motif."""
return self.pwm.log_odds(self._background)

@property
def instances(self):
"""Return the sequences from which the motif was built."""
warnings.warn(
"""The instances attribute has been deprecated. Instead of mymotif.instances, please use mymotif.alignment.sequences.""",
BiopythonDeprecationWarning,
)
if self.alignment is None:
return None
return self.alignment.sequences

def __str__(self, masked=False):
"""Return string representation of a motif."""
text = ""
Expand Down
15 changes: 8 additions & 7 deletions DEPRECATED.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -203,15 +203,16 @@ The ``format`` method of the ``Motif`` class in ``Bio.motifs`` was deprecated
in release 1.77, in favor of a ``__format__`` method that can be used from the
``format`` built-in function. This decision was reversed in release 1.79.
The ``search`` method of the ``Instances`` class in ``Bio.motifs`` was
deprecated in release 1.82. Instead of ``instances.search(sequence)``,
``sequence.search(instances)`` can be used, where sequence is a Seq object.
This allows instances to have different lengths.
deprecated in release 1.82, and removed in release 1.86. Instead of
``instances.search(sequence)``, ``sequence.search(instances)`` can be used,
where sequence is a Seq object. This allows instances to have different lengths.
The ``version`` parameter of the ``weblogo`` method of the ``Motif`` class in
``Bio.motifs`` was deprecated in release 1.83. Using the parameter has no
effect.

The ``Instances`` class and the ``instances`` argument of the ``Motif`` class
initializer in ``Bio.motifs`` were deprecated in release 1.82. Instead of
initializer in ``Bio.motifs`` were deprecated in release 1.82, and removed in
release 1.86. Instead of

>>> from Bio.motifs import Instances
>>> instances = Instances([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')])
Expand All @@ -224,10 +225,10 @@ please use
>>> motif = Motif(alphabet='ACGT', alignment=alignment)

The ``instances`` attribute of the ``Motif`` class in ``Bio.motifs`` was
deprecated in release 1.82. Instead of ``mymotif.instances``, please use
``mymotif.alignment.sequences``.
deprecated in release 1.82, and removed in release 1.86. Instead of
``mymotif.instances``, please use ``mymotif.alignment.sequences``.

The ``Instance`` class in ``Bio.motifs.meme`` was deprecated in release 1.86.
The ``Instance`` class in ``Bio.motifs.meme`` was deprecated in release 1.85.
This class is a subclass from ``Seq``, but does not provide any additional
capabilities. Please use a ``Seq`` object instead.

Expand Down
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