biotite 1.5.0__cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

biotite/sequence/align/alignment.py

@@ -0,0 +1,702 @@
+# 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.align"
+__author__ = "Patrick Kunzmann"
+
+import numbers
+import textwrap
+from collections.abc import Sequence
+import numpy as np
+
+__all__ = [
+    "Alignment",
+    "get_codes",
+    "get_symbols",
+    "get_sequence_identity",
+    "get_pairwise_sequence_identity",
+    "score",
+    "find_terminal_gaps",
+    "remove_terminal_gaps",
+    "remove_gaps",
+]
+
+
+class Alignment(object):
+    """
+    An :class:`Alignment` object stores information about which symbols
+    of *n* sequences are aligned to each other and it stores the
+    corresponding alignment score.
+
+    Instead of saving a list of aligned symbols, this class saves the
+    original *n* sequences, that were aligned, and a so called *trace*,
+    which indicate the aligned symbols of these sequences.
+    The trace is a *(m x n)* :class:`ndarray` with alignment length
+    *m* and sequence count *n*.
+    Each element of the trace is the index in the corresponding
+    sequence.
+    A gap is represented by the value -1.
+
+    Furthermore this class provides multiple utility functions for
+    conversion into strings in order to make the alignment human
+    readable.
+
+    Unless an :class:`Alignment` object is the result of an multiple
+    sequence alignment, the object will contain only two sequences.
+
+    All attributes of this class are publicly accessible.
+
+    Parameters
+    ----------
+    sequences : list
+        A list of aligned sequences.
+    trace : ndarray, dtype=int, shape=(n,m)
+        The alignment trace.
+    score : int, optional
+        Alignment score.
+
+    Attributes
+    ----------
+    sequences : list
+        A list of aligned sequences.
+    trace : ndarray, dtype=int, shape=(n,m)
+        The alignment trace.
+    score : int
+        Alignment score.
+
+    Examples
+    --------
+
+    >>> seq1 = NucleotideSequence("CGTCAT")
+    >>> seq2 = NucleotideSequence("TCATGC")
+    >>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
+    >>> ali = align_optimal(seq1, seq2, matrix)[0]
+    >>> print(ali)
+    CGTCAT--
+    --TCATGC
+    >>> print(ali.trace)
+    [[ 0 -1]
+     [ 1 -1]
+     [ 2  0]
+     [ 3  1]
+     [ 4  2]
+     [ 5  3]
+     [-1  4]
+     [-1  5]]
+    >>> print(ali[1:4].trace)
+    [[ 1 -1]
+     [ 2  0]
+     [ 3  1]]
+    >>> print(ali[1:4, 0:1].trace)
+    [[1]
+     [2]
+     [3]]
+    """
+
+    def __init__(self, sequences, trace, score=None):
+        self.sequences = sequences.copy()
+        self.trace = trace
+        self.score = score
+
+    def __repr__(self):
+        """Represent Alignment a string for debugging."""
+        return (
+            f"Alignment([{', '.join([seq.__repr__() for seq in self.sequences])}], "
+            f"np.{np.array_repr(self.trace)}, score={self.score})"
+        )
+
+    def _gapped_str(self, seq_index):
+        seq_str = ""
+        for i in range(len(self.trace)):
+            j = self.trace[i][seq_index]
+            if j != -1:
+                seq_str += str(self.sequences[seq_index][j])
+            else:
+                seq_str += "-"
+        return seq_str
+
+    def get_gapped_sequences(self):
+        """
+        Get a the string representation of the gapped sequences.
+
+        Returns
+        -------
+        sequences : list of str
+            The list of gapped sequence strings. The order is the same
+            as in `Alignment.sequences`.
+        """
+        return [self._gapped_str(i) for i in range(len(self.sequences))]
+
+    def __str__(self):
+        # Check if any of the sequences
+        # has an non-single letter alphabet
+        all_single_letter = True
+        for seq in self.sequences:
+            if not _is_single_letter(seq.alphabet):
+                all_single_letter = False
+        if all_single_letter:
+            # First dimension: sequence number,
+            # second dimension: line number
+            seq_str_lines_list = []
+            wrapper = textwrap.TextWrapper(break_on_hyphens=False)
+            for i in range(len(self.sequences)):
+                seq_str_lines_list.append(wrapper.wrap(self._gapped_str(i)))
+            ali_str = ""
+            for row_i in range(len(seq_str_lines_list[0])):
+                for seq_j in range(len(seq_str_lines_list)):
+                    ali_str += seq_str_lines_list[seq_j][row_i] + "\n"
+                ali_str += "\n"
+            # Remove final line breaks
+            return ali_str[:-2]
+        else:
+            return super().__str__()
+
+    def __getitem__(self, index):
+        if isinstance(index, tuple):
+            if len(index) > 2:
+                raise IndexError("Only 1D or 2D indices are allowed")
+            if isinstance(index[0], numbers.Integral) or isinstance(
+                index[0], numbers.Integral
+            ):
+                raise IndexError(
+                    "Integers are invalid indices for alignments, "
+                    "a single sequence or alignment column cannot be "
+                    "selected"
+                )
+            return Alignment(
+                Alignment._index_sequences(self.sequences, index[1]),
+                self.trace[index],
+                self.score,
+            )
+        else:
+            return Alignment(self.sequences, self.trace[index], self.score)
+
+    def __iter__(self):
+        raise TypeError("'Alignment' object is not iterable")
+
+    def __len__(self):
+        return len(self.trace)
+
+    def __eq__(self, item):
+        if not isinstance(item, Alignment):
+            return False
+        if self.sequences != item.sequences:
+            return False
+        if not np.array_equal(self.trace, item.trace):
+            return False
+        if self.score != item.score:
+            return False
+        return True
+
+    @staticmethod
+    def _index_sequences(sequences, index):
+        if isinstance(index, (list, tuple)) or (
+            isinstance(index, np.ndarray) and index.dtype != bool
+        ):
+            return [sequences[i] for i in index]
+        elif isinstance(index, np.ndarray) and index.dtype == bool:
+            return [seq for seq, mask in zip(sequences, index) if mask]
+        if isinstance(index, slice):
+            return sequences[index]
+        else:
+            raise IndexError(f"Invalid alignment index type '{type(index).__name__}'")
+
+    @staticmethod
+    def trace_from_strings(seq_str_list):
+        """
+        Create a trace from strings that represent aligned sequences.
+
+        Parameters
+        ----------
+        seq_str_list : list of str
+            The strings, where each each one represents a sequence
+            (with gaps) in an alignment.
+            A ``-`` is interpreted as gap.
+
+        Returns
+        -------
+        trace : ndarray, dtype=int, shape=(n,2)
+            The created trace.
+        """
+        if len(seq_str_list) < 2:
+            raise ValueError("An alignment must contain at least two sequences")
+        seq_i = np.zeros(len(seq_str_list))
+        trace = np.full((len(seq_str_list[0]), len(seq_str_list)), -1, dtype=int)
+        # Get length of string (same length for all strings)
+        # rather than length of list
+        for pos_i in range(len(seq_str_list[0])):
+            for str_j in range(len(seq_str_list)):
+                if seq_str_list[str_j][pos_i] == "-":
+                    trace[pos_i, str_j] = -1
+                else:
+                    trace[pos_i, str_j] = seq_i[str_j]
+                    seq_i[str_j] += 1
+        return trace
+
+
+def get_codes(alignment):
+    """
+    Get the sequence codes of the sequences in the alignment.
+
+    The codes are built from the trace:
+    Instead of the indices of the aligned symbols (trace), the return
+    value contains the corresponding symbol codes for each index.
+    Gaps are still represented by *-1*.
+
+    Parameters
+    ----------
+    alignment : Alignment
+        The alignment to get the sequence codes for.
+
+    Returns
+    -------
+    codes : ndarray, dtype=int, shape=(n,m)
+        The sequence codes for the alignment.
+        The shape is *(n,m)* for *n* sequences and *m* alignment cloumn.
+        The array uses *-1* values for gaps.
+
+    Examples
+    --------
+
+    >>> seq1 = NucleotideSequence("CGTCAT")
+    >>> seq2 = NucleotideSequence("TCATGC")
+    >>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
+    >>> ali = align_optimal(seq1, seq2, matrix)[0]
+    >>> print(ali)
+    CGTCAT--
+    --TCATGC
+    >>> print(get_codes(ali))
+    [[ 1  2  3  1  0  3 -1 -1]
+     [-1 -1  3  1  0  3  2  1]]
+    """
+    trace = alignment.trace
+    sequences = alignment.sequences
+
+    # The number of sequences is the first dimension
+    codes = np.zeros((trace.shape[1], trace.shape[0]), dtype=np.int64)
+    for i in range(len(sequences)):
+        # Mark -1 explicitly as int64 to avoid that the unsigned dtype
+        # of the sequence code is used
+        # (https://numpy.org/neps/nep-0050-scalar-promotion.html)
+        codes[i] = np.where(
+            trace[:, i] != -1, sequences[i].code[trace[:, i]], np.int64(-1)
+        )
+
+    return np.stack(codes)
+
+
+def get_symbols(alignment):
+    """
+    Similar to :func:`get_codes()`, but contains the decoded symbols
+    instead of codes.
+    Gaps are still represented by *None* values.
+
+    Parameters
+    ----------
+    alignment : Alignment
+        The alignment to get the symbols for.
+
+    Returns
+    -------
+    symbols : list of list
+        The nested list of symbols.
+
+    See Also
+    --------
+    get_codes : Get the sequence codes of the sequences in the alignment.
+
+    Examples
+    --------
+
+    >>> seq1 = NucleotideSequence("CGTCAT")
+    >>> seq2 = NucleotideSequence("TCATGC")
+    >>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
+    >>> ali = align_optimal(seq1, seq2, matrix)[0]
+    >>> print(ali)
+    CGTCAT--
+    --TCATGC
+    >>> print(get_symbols(ali))
+    [['C', 'G', 'T', 'C', 'A', 'T', None, None], [None, None, 'T', 'C', 'A', 'T', 'G', 'C']]
+    """
+    codes = get_codes(alignment)
+    symbols = [None] * codes.shape[0]
+    for i in range(codes.shape[0]):
+        alphabet = alignment.sequences[i].get_alphabet()
+        codes_wo_gaps = codes[i, codes[i] != -1]
+        symbols_wo_gaps = alphabet.decode_multiple(codes_wo_gaps)
+        if isinstance(symbols_wo_gaps, np.ndarray):
+            symbols_wo_gaps = symbols_wo_gaps.tolist()
+        symbols_for_seq = np.full(len(codes[i]), None, dtype=object)
+        symbols_for_seq[codes[i] != -1] = symbols_wo_gaps
+        symbols[i] = symbols_for_seq.tolist()
+    return symbols
+
+
+def get_sequence_identity(alignment, mode="not_terminal"):
+    """
+    Calculate the sequence identity for an alignment.
+
+    The identity is equal to the matches divided by a measure for the
+    length of the alignment that depends on the `mode` parameter.
+
+    Parameters
+    ----------
+    alignment : Alignment
+        The alignment to calculate the identity for.
+    mode : {'all', 'not_terminal', 'shortest'}, optional
+        The calculation mode for alignment length.
+
+            - **all** - The number of matches divided by the number of
+              all alignment columns.
+            - **not_terminal** - The number of matches divided by the
+              number of alignment columns that are not terminal gaps in
+              any of the sequences.
+            - **shortest** - The number of matches divided by the
+              length of the shortest sequence.
+
+        Default is *not_terminal*.
+
+    Returns
+    -------
+    identity : float
+        The sequence identity, ranging between 0 and 1.
+
+    See Also
+    --------
+    get_pairwise_sequence_identity : Get sequence identity for each pair of alignment rows.
+    """
+    codes = get_codes(alignment)
+
+    # Count matches
+    matches = 0
+    for i in range(codes.shape[1]):
+        column = codes[:, i]
+        # One unique value -> all symbols match
+        unique_symbols = np.unique(column)
+        if len(unique_symbols) == 1 and unique_symbols[0] != -1:
+            matches += 1
+
+    # Calculate length
+    if mode == "all":
+        length = len(alignment)
+    elif mode == "not_terminal":
+        start, stop = find_terminal_gaps(alignment)
+        if stop <= start:
+            raise ValueError(
+                "Cannot calculate non-terminal identity, "
+                "at least two sequences have no overlap"
+            )
+        length = stop - start
+    elif mode == "shortest":
+        length = min([len(seq) for seq in alignment.sequences])
+    else:
+        raise ValueError(f"'{mode}' is an invalid calculation mode")
+
+    return matches / length
+
+
+def get_pairwise_sequence_identity(alignment, mode="not_terminal"):
+    """
+    Calculate the pairwise sequence identity for an alignment.
+
+    The identity is equal to the matches divided by a measure for the
+    length of the alignment that depends on the `mode` parameter.
+
+    Parameters
+    ----------
+    alignment : Alignment, length=n
+        The alignment to calculate the pairwise sequence identity for.
+    mode : {'all', 'not_terminal', 'shortest'}, optional
+        The calculation mode for alignment length.
+
+            - **all** - The number of matches divided by the number of
+              all alignment columns.
+            - **not_terminal** - The number of matches divided by the
+              number of alignment columns that are not terminal gaps in
+              any of the two considered sequences.
+            - **shortest** - The number of matches divided by the
+              length of the shortest one of the two sequences.
+
+        Default is *not_terminal*.
+
+    Returns
+    -------
+    identity : ndarray, dtype=float, shape=(n,n)
+        The pairwise sequence identity, ranging between 0 and 1.
+
+    See Also
+    --------
+    get_sequence_identity : Get sequence identity over all alignment rows.
+    """
+    codes = get_codes(alignment)
+    n_seq = len(codes)
+
+    # Count matches
+    # Calculate at which positions the sequences are identical
+    # and are not gaps
+    equality_matrix = (
+        (codes[:, np.newaxis, :] == codes[np.newaxis, :, :])
+        & (codes[:, np.newaxis, :] != -1)
+        & (codes[np.newaxis, :, :] != -1)
+    )
+    # Sum these positions up
+    matches = np.count_nonzero(equality_matrix, axis=-1)
+
+    # Calculate length
+    if mode == "all":
+        length = len(alignment)
+    elif mode == "not_terminal":
+        length = np.zeros((n_seq, n_seq))
+        for i in range(n_seq):
+            for j in range(n_seq):
+                # Find latest start and earliest stop of all sequences
+                start, stop = find_terminal_gaps(alignment[:, [i, j]])
+                if stop <= start:
+                    raise ValueError(
+                        "Cannot calculate non-terminal identity, "
+                        "as the two sequences have no overlap"
+                    )
+                length[i, j] = stop - start
+    elif mode == "shortest":
+        length = np.zeros((n_seq, n_seq))
+        for i in range(n_seq):
+            for j in range(n_seq):
+                length[i, j] = min(
+                    [len(alignment.sequences[i]), len(alignment.sequences[j])]
+                )
+    else:
+        raise ValueError(f"'{mode}' is an invalid calculation mode")
+
+    return matches / length
+
+
+def score(alignment, matrix, gap_penalty=-10, terminal_penalty=True):
+    """
+    Calculate the similarity score of an alignment.
+
+    If the alignment contains more than two sequences,
+    all pairwise scores are counted.
+
+    Parameters
+    ----------
+    alignment : Alignment
+        The alignment to calculate the identity for.
+    matrix : SubstitutionMatrix
+        The substitution matrix used for scoring.
+    gap_penalty : int or (tuple, dtype=int), optional
+        If an integer is provided, the value will be interpreted as
+        general gap penalty. If a tuple is provided, an affine gap
+        penalty is used. The first integer in the tuple is the gap
+        opening penalty, the second integer is the gap extension
+        penalty.
+        The values need to be negative.
+    terminal_penalty : bool, optional
+        If true, gap penalties are applied to terminal gaps.
+
+    Returns
+    -------
+    score : int
+        The similarity score.
+    """
+    codes = get_codes(alignment)
+    matrix = matrix.score_matrix()
+
+    # Sum similarity scores (without gaps)
+    score = 0
+    # Iterate over all positions
+    for pos in range(codes.shape[1]):
+        column = codes[:, pos]
+        # Iterate over all possible pairs
+        # Do not count self-similarity
+        # and do not count similarity twice (not S(i,j) and S(j,i))
+        for i in range(codes.shape[0]):
+            for j in range(i + 1, codes.shape[0]):
+                code_i = column[i]
+                code_j = column[j]
+                # Ignore gaps
+                if code_i != -1 and code_j != -1:
+                    score += matrix[code_i, code_j]
+
+    # Sum gap penalties
+    if isinstance(gap_penalty, numbers.Real):
+        gap_open = gap_penalty
+        gap_ext = gap_penalty
+    elif isinstance(gap_penalty, Sequence):
+        gap_open = gap_penalty[0]
+        gap_ext = gap_penalty[1]
+    else:
+        raise TypeError("Gap penalty must be either integer or tuple")
+    # Iterate over all sequences
+    for seq_code in codes:
+        in_gap = False
+        if terminal_penalty:
+            start_index = 0
+            stop_index = len(seq_code)
+        else:
+            # Find a start and stop index excluding terminal gaps
+            start_index, stop_index = find_terminal_gaps(alignment)
+        for i in range(start_index, stop_index):
+            if seq_code[i] == -1:
+                if in_gap:
+                    score += gap_ext
+                else:
+                    score += gap_open
+                in_gap = True
+            else:
+                in_gap = False
+    return score
+
+
+def find_terminal_gaps(alignment):
+    """
+    Find the slice indices that would remove terminal gaps from an
+    alignment.
+
+    Terminal gaps are gaps that appear before all sequences start and
+    after any sequence ends.
+
+    Parameters
+    ----------
+    alignment : Alignment
+        The alignment, where the slice indices should be found in.
+
+    Returns
+    -------
+    start, stop : int
+        Indices that point to the start and exclusive stop of the
+        alignment columns without terminal gaps.
+        When these indices are used as slice index for an alignment or
+        trace, the index would remove terminal gaps.
+
+    See Also
+    --------
+    remove_terminal_gaps : Remove terminal gap columns directly.
+
+    Examples
+    --------
+
+    >>> sequences = [
+    ...     NucleotideSequence(seq_string) for seq_string in (
+    ...         "AAAAACTGATTC",
+    ...         "AAACTGTTCA",
+    ...         "CTGATTCAAA"
+    ...     )
+    ... ]
+    >>> trace = np.transpose([
+    ...     ( 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, -1, -1, -1),
+    ...     (-1, -1,  0,  1,  2,  3,  4,  5, -1,  6,  7,  8,  9, -1, -1),
+    ...     (-1, -1, -1, -1, -1,  0,  1,  2,  3,  4,  5,  6,  7,  8,  9),
+    ... ])
+    >>> alignment = Alignment(sequences, trace)
+    >>> print(alignment)
+    AAAAACTGATTC---
+    --AAACTG-TTCA--
+    -----CTGATTCAAA
+    >>> print(find_terminal_gaps(alignment))
+    (5, 12)
+    """
+    trace = alignment.trace
+    # Find for each sequence the positions of non-gap symbols
+    no_gap_pos = [np.where(trace[:, i] != -1)[0] for i in range(trace.shape[1])]
+    # Find for each sequence the positions of the sequence start and end
+    # in the alignment
+    firsts = [no_gap_pos[i][0] for i in range(trace.shape[1])]
+    lasts = [no_gap_pos[i][-1] for i in range(trace.shape[1])]
+    # The terminal gaps are before all sequences start and after any
+    # sequence ends
+    # Use exclusive stop -> -1
+    return np.max(firsts).item(), np.min(lasts).item() + 1
+
+
+def remove_terminal_gaps(alignment):
+    """
+    Remove terminal gaps from an alignment.
+
+    Terminal gaps are gaps that appear before all sequences start and
+    after any sequence ends.
+
+    Parameters
+    ----------
+    alignment : Alignment
+        The alignment, where the terminal gaps should be removed from.
+
+    Returns
+    -------
+    truncated_alignment : Alignment
+        A shallow copy of the input `alignment` with an truncated trace,
+        that does not contain alignment columns with terminal gaps.
+
+    See Also
+    --------
+    find_terminal_gaps : Only find terminal gap columns.
+
+    Examples
+    --------
+
+    >>> sequences = [
+    ...     NucleotideSequence(seq_string) for seq_string in (
+    ...         "AAAAACTGATTC",
+    ...         "AAACTGTTCA",
+    ...         "CTGATTCAAA"
+    ...     )
+    ... ]
+    >>> trace = np.transpose([
+    ...     ( 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, -1, -1, -1),
+    ...     (-1, -1,  0,  1,  2,  3,  4,  5, -1,  6,  7,  8,  9, -1, -1),
+    ...     (-1, -1, -1, -1, -1,  0,  1,  2,  3,  4,  5,  6,  7,  8,  9),
+    ... ])
+    >>> alignment = Alignment(sequences, trace)
+    >>> print(alignment)
+    AAAAACTGATTC---
+    --AAACTG-TTCA--
+    -----CTGATTCAAA
+    >>> truncated_alignment = remove_terminal_gaps(alignment)
+    >>> print(truncated_alignment)
+    CTGATTC
+    CTG-TTC
+    CTGATTC
+    """
+    start, stop = find_terminal_gaps(alignment)
+    if stop < start:
+        raise ValueError(
+            "Cannot remove terminal gaps, since at least two sequences have "
+            "no overlap and the resulting alignment would be empty"
+        )
+    return alignment[start:stop]
+
+
+def remove_gaps(alignment):
+    """
+    Remove all gap columns from an alignment.
+
+    Parameters
+    ----------
+    alignment : Alignment
+        The alignment to be modified.
+
+    Returns
+    -------
+    truncated_alignment : Alignment
+        The alignment without gap columns.
+
+    See Also
+    --------
+    remove_terminal_gaps : Remove only terminal gap columns.
+    """
+    non_gap_mask = (alignment.trace != -1).all(axis=1)
+    return alignment[non_gap_mask]
+
+
+def _is_single_letter(alphabet):
+    """
+    More relaxed version of :func:`biotite.sequence.alphabet.is_letter_alphabet()`:
+    It is sufficient that only only the string representation of each symbol is only
+    a single character.
+    """
+    if alphabet.is_letter_alphabet():
+        return True
+    for symbol in alphabet:
+        if len(str(symbol)) != 1:
+            return False
+    return True