biotite 1.1.0__cp313-cp313-macosx_10_13_x86_64.whl

biotite/sequence/profile.py

@@ -0,0 +1,567 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+import warnings
+from numbers import Integral
+import numpy as np
+from biotite.sequence.align.alignment import get_codes
+from biotite.sequence.alphabet import LetterAlphabet
+from biotite.sequence.seqtypes import (
+    GeneralSequence,
+    NucleotideSequence,
+    ProteinSequence,
+)
+
+__name__ = "biotite.sequence"
+__author__ = "Maximilian Greil"
+__all__ = ["SequenceProfile"]
+
+# Abbreviations
+_NUC_DNA_ALPH = NucleotideSequence.alphabet_unamb
+_NUC_RNA_ALPH = LetterAlphabet(["A", "C", "G", "U"])
+_PROT_ALPH = ProteinSequence.alphabet
+
+
+def _determine_common_alphabet(alphabets):
+    """
+    Determine the common alphabet from a list of alphabets, that
+    extends all alphabets.
+    """
+    common_alphabet = alphabets[0]
+    for alphabet in alphabets[1:]:
+        if not common_alphabet.extends(alphabet):
+            if alphabet.extends(common_alphabet):
+                common_alphabet = alphabet
+            else:
+                raise ValueError(
+                    "There is no common alphabet that extends all alphabets"
+                )
+    return common_alphabet
+
+
+def _codes_to_iupac(frequency, codes, maxes, row):
+    """
+    Returns IUPAC code for a row of 'symbols' with none, one or
+    multiple maximum positions.
+    """
+    if np.sum(frequency) == 0:
+        raise ValueError(
+            f"There is an empty column in the 'symbols' frequency table. "
+            f"This doesn't make sense in context of an alignment. "
+            f"Please check the 'symbols' frequency table in row {row}."
+        )
+    key = tuple(np.where(frequency == maxes)[0])
+    return codes[key]
+
+
+class SequenceProfile(object):
+    """
+    A :class:`SequenceProfile` object stores information about a
+    sequence profile of aligned sequences.
+    It is possible to calculate and return its consensus sequence.
+
+    This class saves the position frequency matrix
+    (position count matrix) 'symbols' of the occurrences of each
+    alphabet symbol at each position.
+    It also saves the number of gaps at each position in the array
+    'gaps'.
+
+    With :meth:`from_alignment()` a :class:`SequenceProfile` object can
+    be created from an indefinite number of aligned sequences.
+
+    With :meth:`probability_matrix()` the position probability matrix
+    can be created based on 'symbols' and a pseudocount.
+
+    With :meth:`log_odds_matrix()` the position weight matrix can
+    be created based on the before calculated position probability
+    matrix and the background frequencies.
+
+    With :meth:`sequence_probability_from_matrix()` the probability of a
+    sequence can be calculated based on the before calculated position
+    probability matrix of this instance of object SequenceProfile.
+
+    With :meth:`sequence_score_from_matrix()` the score of a sequence
+    can be calculated based on the before calculated position weight
+    matrix of this instance of object SequenceProfile.
+
+    All attributes of this class are publicly accessible.
+
+    Parameters
+    ----------
+    symbols : ndarray, dtype=int, shape=(n,k)
+        This matrix simply saves for each position how often absolutely
+        each symbol is present.
+    gaps : ndarray, dtype=int, shape=n
+        Array which indicates the number of gaps at each position.
+    alphabet : Alphabet, length=k
+        Alphabet of sequences of sequence profile
+
+    Attributes
+    ----------
+    symbols : ndarray, dtype=int, shape=(n,k)
+        This matrix simply saves for each position how often absolutely
+        each symbol is present.
+    gaps : ndarray, dtype=int, shape=n
+        Array which indicates the number of gaps at each position.
+    alphabet : Alphabet, length=k
+        Alphabet of sequences of sequence profile
+
+    Examples
+    --------
+
+    Create a profile from a multiple sequence alignment:
+
+    >>> sequences = [
+    ...     NucleotideSequence("CGCTCATTC"),
+    ...     NucleotideSequence("CGCTATTC"),
+    ...     NucleotideSequence("CCCTCAATC"),
+    ... ]
+    >>> msa, _, _, _ = align_multiple(
+    ...     sequences, SubstitutionMatrix.std_nucleotide_matrix(), gap_penalty=-5
+    ... )
+    >>> print(msa)
+    CGCTCATTC
+    CGCT-ATTC
+    CCCTCAATC
+    >>> profile = SequenceProfile.from_alignment(msa)
+    >>> print(profile)
+      A C G T
+    0 0 3 0 0
+    1 0 1 2 0
+    2 0 3 0 0
+    3 0 0 0 3
+    4 0 2 0 0
+    5 3 0 0 0
+    6 1 0 0 2
+    7 0 0 0 3
+    8 0 3 0 0
+    >>> print(profile.gaps)
+    [0 0 0 0 1 0 0 0 0]
+
+    Slice the profile (masks and index arrays are also supported):
+
+    >>> print(profile[2:])
+      A C G T
+    0 0 3 0 0
+    1 0 0 0 3
+    2 0 2 0 0
+    3 3 0 0 0
+    4 1 0 0 2
+    5 0 0 0 3
+    6 0 3 0 0
+
+    Use the profile to compute the position probability matrix:
+
+    >>> print(profile.probability_matrix())
+    [[0.000 1.000 0.000 0.000]
+     [0.000 0.333 0.667 0.000]
+     [0.000 1.000 0.000 0.000]
+     [0.000 0.000 0.000 1.000]
+     [0.000 1.000 0.000 0.000]
+     [1.000 0.000 0.000 0.000]
+     [0.333 0.000 0.000 0.667]
+     [0.000 0.000 0.000 1.000]
+     [0.000 1.000 0.000 0.000]]
+    """
+
+    def __init__(self, symbols, gaps, alphabet):
+        self._symbols = symbols
+        self._gaps = gaps
+        self._alphabet = alphabet
+
+        if len(alphabet) != symbols.shape[1]:
+            raise ValueError(
+                f"The given alphabet doesn't have the same length "
+                f"({len(alphabet)}) as the number of columns "
+                f"({symbols.shape[1]}) in the 'symbols' frequency table."
+            )
+
+        if gaps.shape[0] != symbols.shape[0]:
+            raise ValueError(
+                f"The given 'gaps' position matrix doesn't have the same "
+                f"length ({gaps.shape[0]}) as the 'symbols' "
+                f"frequency table ({symbols.shape[0]})"
+            )
+
+    @property
+    def symbols(self):
+        return self._symbols
+
+    @property
+    def gaps(self):
+        return self._gaps
+
+    @property
+    def alphabet(self):
+        return self._alphabet
+
+    @symbols.setter
+    def symbols(self, new_symbols):
+        if not new_symbols.shape == self.symbols.shape:
+            raise ValueError(
+                f"New ndarray 'symbols' must be of same shape "
+                f"{self.symbols.shape} as the old one"
+            )
+        self._symbols = new_symbols
+
+    @gaps.setter
+    def gaps(self, new_gaps):
+        if not new_gaps.shape == self.gaps.shape:
+            raise ValueError(
+                f"New ndarray 'gaps' must be of same shape "
+                f"{self.gaps.shape} as the old one"
+            )
+        self._gaps = new_gaps
+
+    def __str__(self):
+        # Add an additional row and column for the position and symbol indicators
+        print_matrix = np.full(
+            (self.symbols.shape[0] + 1, self.symbols.shape[1] + 1), "", dtype=object
+        )
+        print_matrix[1:, 1:] = self.symbols.astype(str)
+        print_matrix[0, 1:] = [str(sym) for sym in self.alphabet]
+        print_matrix[1:, 0] = [str(i) for i in range(self.symbols.shape[0])]
+        max_len = len(max(print_matrix.flatten(), key=len))
+        return "\n".join(
+            [
+                " ".join([str(cell).rjust(max_len) for cell in row])
+                for row in print_matrix
+            ]
+        )
+
+    def __repr__(self):
+        return (
+            f"SequenceProfile(np.{np.array_repr(self.symbols)}, "
+            f"np.{np.array_repr(self.gaps)}, Alphabet({self.alphabet}))"
+        )
+
+    def __eq__(self, item):
+        if not isinstance(item, SequenceProfile):
+            return False
+        if not np.array_equal(self.symbols, item.symbols):
+            return False
+        if not np.array_equal(self.gaps, item.gaps):
+            return False
+        if not self.alphabet == item.alphabet:
+            return False
+        return True
+
+    @staticmethod
+    def from_alignment(alignment, alphabet=None):
+        """
+        Get an object of :class:`SequenceProfile` from an object of
+        :class:`Alignment`.
+
+        Based on the sequences of the alignment, the SequenceProfile
+        parameters symbols and gaps are calculated.
+
+        Parameters
+        ----------
+        alignment : Alignment
+            An Alignment object to create the SequenceProfile object
+            from.
+        alphabet : bool
+            This alphabet will be used when creating the SequenceProfile
+            object. If no alphabet is selected, the alphabet for this
+            SequenceProfile
+            object will be calculated from the sequences of object
+            Alignment.
+            (Default: None).
+
+        Returns
+        -------
+        profile: SequenceProfile
+            The created SequenceProfile object
+        """
+        sequences = get_codes(alignment)
+        if alphabet is None:
+            alphabet = _determine_common_alphabet(
+                [seq.alphabet for seq in alignment.sequences]
+            )
+        else:
+            for alph in (seq.alphabet for seq in alignment.sequences):
+                if not alphabet.extends(alph):
+                    raise ValueError(
+                        "The given alphabet is incompatible with a least one "
+                        "alphabet of the given sequences"
+                    )
+        symbols = np.zeros((len(sequences[0]), len(alphabet)), dtype=int)
+        gaps = np.zeros(len(sequences[0]), dtype=int)
+        sequences = np.transpose(sequences)
+        for i in range(len(sequences)):
+            row = np.where(sequences[i,] == -1, len(alphabet), sequences[i,])
+            count = np.bincount(row, minlength=len(alphabet) + 1)
+            symbols[i,] = count[0 : len(alphabet)]
+            gaps[i] = count[-1]
+        return SequenceProfile(symbols, gaps, alphabet)
+
+    def to_consensus(self, as_general=False):
+        """
+        Get the consensus sequence for this SequenceProfile object.
+
+        Parameters
+        ----------
+        as_general : bool
+            If true, returns consensus sequence as GeneralSequence
+            object.
+            Otherwise, the consensus sequence object type is chosen
+            based on the alphabet of this SequenceProfile object
+            (Default: False).
+
+        Returns
+        -------
+        consensus: Sequence
+            The calculated consensus sequence
+        """
+        # https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes
+        if as_general:
+            return self._general_to_consensus()
+        elif self.alphabet == _NUC_DNA_ALPH:
+            return NucleotideSequence(self._dna_to_consensus())
+        elif self.alphabet == _NUC_RNA_ALPH:
+            return NucleotideSequence(self._rna_to_consensus())
+        elif self.alphabet == _PROT_ALPH:
+            return self._prot_to_consensus()
+        return self._general_to_consensus()
+
+    def _dna_to_consensus(self):
+        codes = {
+            (0,): "A",
+            (1,): "C",
+            (2,): "G",
+            (3,): "T",
+            (0, 2): "R",
+            (1, 3): "Y",
+            (1, 2): "S",
+            (0, 3): "W",
+            (2, 3): "K",
+            (0, 1): "M",
+            (1, 2, 3): "B",
+            (0, 2, 3): "D",
+            (0, 1, 3): "H",
+            (0, 1, 2): "V",
+            (0, 1, 2, 3): "N",
+        }
+        consensus = ""
+        maxes = np.max(self.symbols, axis=1)
+        for i in range(len(self.symbols)):
+            consensus += _codes_to_iupac(self.symbols[i, :], codes, maxes[i], i)
+        return consensus
+
+    def _rna_to_consensus(self):
+        codes = {
+            (0,): "A",
+            (1,): "C",
+            (2,): "G",
+            (3,): "U",
+            (0, 2): "R",
+            (1, 3): "Y",
+            (1, 2): "S",
+            (0, 3): "W",
+            (2, 3): "K",
+            (0, 1): "M",
+            (1, 2, 3): "B",
+            (0, 2, 3): "D",
+            (0, 1, 3): "H",
+            (0, 1, 2): "V",
+            (0, 1, 2, 3): "N",
+        }
+        consensus = ""
+        maxes = np.max(self.symbols, axis=1)
+        for i in range(len(self.symbols)):
+            consensus += _codes_to_iupac(self.symbols[i, :], codes, maxes[i], i)
+        return consensus
+
+    def _prot_to_consensus(self):
+        """
+        In case there is more than one symbol with the same maximal
+        occurrences, the alphabetically sorted first symbol will be
+        taken for the consensus sequence.
+        """
+        consensus = ProteinSequence()
+        consensus.code = np.argmax(self.symbols, axis=1)
+        consensus.code = np.where(
+            np.sum(self.symbols, axis=1) == 0, 23, consensus.code
+        )  # _PROT_ALPH[23] = 'X'
+        return consensus
+
+    def _general_to_consensus(self):
+        """
+        In case there is more than one symbol with the same maximal
+        occurrences, the alphabetically sorted first symbol will be
+        taken for the consensus sequence.
+        In case the sum of occurrences of all symbols at a position is
+        zero, the alphabetically sorted first symbol will be taken for
+        the consensus sequence.
+        """
+        consensus = GeneralSequence(self.alphabet)
+        consensus.code = np.argmax(self.symbols, axis=1)
+        return consensus
+
+    def probability_matrix(self, pseudocount=0):
+        r"""
+        Calculate the position probability matrix (PPM) based on
+        'symbols' and the given pseudocount.
+        This new matrix has the same shape as 'symbols'.
+
+        .. math::
+
+            P(S) = \frac {C_S + \frac{c_p}{k}} {\sum_{i} C_i + c_p}
+
+        :math:`S`: The symbol.
+
+        :math:`C_S`: The count of symbol :math:`S` at the sequence
+        position.
+
+        :math:`c_p`: The pseudocount.
+
+        :math:`k`: Length of the alphabet.
+
+        Parameters
+        ----------
+        pseudocount: int, optional
+            Amount added to the number of observed cases in order to
+            change the expected probability of the PPM.
+            (Default: 0)
+
+        Returns
+        -------
+        ppm: ndarray, dtype=float, shape=(n,k)
+            The calculated the position probability matrix.
+        """
+        if pseudocount < 0:
+            raise ValueError("Pseudocount can not be smaller than zero.")
+        return (self.symbols + pseudocount / self.symbols.shape[1]) / (
+            np.sum(self.symbols, axis=1)[:, np.newaxis] + pseudocount
+        )
+
+    def log_odds_matrix(self, background_frequencies=None, pseudocount=0):
+        r"""
+        Calculate the position weight matrix (PWM) based on the
+        position probability matrix (PPM) (with given pseudocount) and
+        background_frequencies.
+        This new matrix has the same shape as 'symbols'.
+
+        .. math::
+
+            W(S) = \log_2 \left( \frac{P(S)}{B_S} \right)
+
+        :math:`S`: The symbol.
+
+        :math:`P(S)`: The probability of symbol :math:`S` at the
+        sequence position.
+
+        :math:`c_p`: The background frequency of symbol :math:`S`.
+
+        Parameters
+        ----------
+        pseudocount: int, optional
+            Amount added to the number of observed cases in order to change
+            the expected probability of the PPM.
+            (Default: 0)
+        background_frequencies: ndarray, shape=(k,), dtype=float, optional
+            The background frequencies for each symbol in the alphabet.
+            By default, a uniform distribution is assumed.
+
+        Returns
+        -------
+        pwm: ndarray, dtype=float, shape=(n,k)
+            The calculated the position weight matrix.
+        """
+        if background_frequencies is None:
+            background_frequencies = 1 / len(self.alphabet)
+        ppm = self.probability_matrix(pseudocount=pseudocount)
+        # Catch warning that appears, if a symbol is missing at any
+        # position in the profile
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore", category=RuntimeWarning)
+            return np.log2(ppm / background_frequencies)
+
+    def sequence_probability(self, sequence, pseudocount=0):
+        r"""
+        Calculate probability of a sequence based on the
+        position probability matrix (PPM).
+
+        The sequence probability is the product of the probability of
+        the respective symbol over all sequence positions.
+
+        Parameters
+        ----------
+        sequence : Sequence
+           The input sequence.
+        pseudocount: int, optional
+            Amount added to the number of observed cases in order to change
+            the expected probability of the PPM.
+            (Default: 0)
+
+        Returns
+        -------
+        probability: float
+           The calculated probability for the input sequence based on
+           the PPM.
+        """
+        ppm = self.probability_matrix(pseudocount=pseudocount)
+        if len(sequence) != len(ppm):
+            raise ValueError(
+                f"The given sequence has a different length ({len(sequence)}) than "
+                f"the position probability matrix ({len(ppm)})."
+            )
+        if not ppm.shape == self.symbols.shape:
+            raise ValueError(
+                f"Position probability matrix {ppm.shape} must be of same shape "
+                f"as 'symbols' {self.symbols.shape}"
+            )
+        return np.prod(ppm[np.arange(len(sequence)), sequence.code])
+
+    def sequence_score(self, sequence, background_frequencies=None, pseudocount=0):
+        """
+        Calculate score of a sequence based on the
+        position weight matrix (PWM).
+
+        The score is the sum of weights (log-odds scores) of
+        the respective symbol over all sequence positions.
+
+        Parameters
+        ----------
+        sequence : Sequence
+           The input sequence.
+        pseudocount: int, optional
+            Amount added to the number of observed cases in order to change
+            the expected probability of the PPM.
+            (Default: 0)
+        background_frequencies: ndarray, shape=(k,), dtype=float, optional
+            The background frequencies for each symbol in the alphabet.
+            By default a uniform distribution is assumed.
+
+        Returns
+        -------
+        score: float
+           The calculated score for the input sequence based on
+           the PWM.
+        """
+        if background_frequencies is None:
+            background_frequencies = 1 / len(self.alphabet)
+        pwm = self.log_odds_matrix(
+            background_frequencies=background_frequencies, pseudocount=pseudocount
+        )
+        if len(sequence) != len(pwm):
+            raise ValueError(
+                f"The given sequence has a different length ({len(sequence)}) than "
+                f"the position weight matrix ({len(pwm)})."
+            )
+        if not pwm.shape == self.symbols.shape:
+            raise ValueError(
+                f"Position weight matrix {pwm.shape} must be of same shape "
+                f"as 'symbols' {self.symbols.shape}"
+            )
+        return np.sum(pwm[np.arange(len(sequence)), sequence.code])
+
+    def __getitem__(self, index):
+        if isinstance(index, Integral):
+            # Do not allow to collapse dimensions
+            index = slice(index, index + 1)
+        return SequenceProfile(self.symbols[index], self.gaps[index], self.alphabet)
+
+    def __len__(self):
+        return len(self.symbols)

biotite/sequence/search.py

@@ -0,0 +1,118 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__name__ = "biotite.sequence"
+__author__ = "Patrick Kunzmann"
+__all__ = ["find_subsequence", "find_symbol", "find_symbol_first", "find_symbol_last"]
+
+import numpy as np
+
+
+def find_subsequence(sequence, query):
+    """
+    Find a subsequence in a sequence.
+
+    Parameters
+    ----------
+    sequence : Sequence
+        The sequence to find the subsequence in.
+    query : Sequence
+        The potential subsequence. Its alphabet must extend the
+        `sequence` alphabet.
+
+    Returns
+    -------
+    match_indices : ndarray
+        The starting indices in `sequence`, where `query` has been
+        found. The array is empty if no match has been found.
+
+    Raises
+    ------
+    ValueError
+        If the `query` alphabet does not extend the `sequence` alphabet.
+
+    Examples
+    --------
+
+    >>> main_seq = NucleotideSequence("ACTGAATGA")
+    >>> sub_seq = NucleotideSequence("TGA")
+    >>> print(find_subsequence(main_seq, sub_seq))
+    [2 6]
+
+    """
+    if not sequence.get_alphabet().extends(query.get_alphabet()):
+        raise ValueError("The sequences alphabets are not equal")
+    match_indices = []
+    frame_size = len(query)
+    for i in range(len(sequence) - frame_size + 1):
+        sub_seq_code = sequence.code[i : i + frame_size]
+        if np.array_equal(query.code, sub_seq_code):
+            match_indices.append(i)
+    return np.array(match_indices)
+
+
+def find_symbol(sequence, symbol):
+    """
+    Find a symbol in a sequence.
+
+    Parameters
+    ----------
+    sequence : Sequence
+        The sequence to find the symbol in.
+    symbol : object
+        The symbol to be found in `sequence`.
+
+    Returns
+    -------
+    match_indices : ndarray
+        The indices in `sequence`, where `symbol` has been found.
+    """
+    code = sequence.get_alphabet().encode(symbol)
+    return np.where(sequence.code == code)[0]
+
+
+def find_symbol_first(sequence, symbol):
+    """
+    Find first occurence of a symbol in a sequence.
+
+    Parameters
+    ----------
+    sequence : Sequence
+        The sequence to find the symbol in.
+    symbol : object
+        The symbol to be found in `sequence`.
+
+    Returns
+    -------
+    first_index : int
+        The first index of `symbol` in `sequence`. If `symbol` is not in
+        `sequence`, -1 is returned.
+    """
+    match_i = find_symbol(sequence, symbol)
+    if len(match_i) == 0:
+        return -1
+    return np.min(match_i)
+
+
+def find_symbol_last(sequence, symbol):
+    """
+    Find last occurence of a symbol in a sequence.
+
+    Parameters
+    ----------
+    sequence : Sequence
+        The sequence to find the symbol in.
+    symbol : object
+        The symbol to be found in `sequence`.
+
+    Returns
+    -------
+    flast_index : int
+        The last index of `symbol` in `sequence`. If `symbol` is not in
+        `sequence`, -1 is returned.
+    """
+    match_i = find_symbol(sequence, symbol)
+    if len(match_i) == 0:
+        return -1
+    return np.max(match_i)