biotite 1.5.0__cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

biotite/sequence/codec.pyx

@@ -0,0 +1,155 @@
+# 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__ = ["encode_chars", "decode_to_chars", "map_sequence_code"]
+
+cimport cython
+cimport numpy as np
+
+import numpy as np
+
+
+ctypedef np.int64_t int64
+ctypedef np.uint8_t uint8
+ctypedef np.uint16_t uint16
+ctypedef np.uint32_t uint32
+ctypedef np.uint64_t uint64
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+def encode_chars(const unsigned char[:] alphabet not None,
+                 const unsigned char[:] symbols not None):
+    """
+    Encode an array of symbols into an array of symbol codes.
+
+    Only works for symbols that are printable ASCII characters.
+
+    Parameters
+    ----------
+    alphabet : ndarray, shape=(n,), dtype="|S1"
+        The alphabet as array.
+        It is indexed via ASCII values and the corresponding values are
+        the symbol codes.
+    symbols : ndarray, dtype="|S1"
+        The symbols (ASCII characters) to be encoded.
+    
+    Returns
+    -------
+    code : ndarray, shape=(n,), dtype="|S1"
+        The encoded symbols.
+    """
+    cdef int i
+    # The last symbol code of the alphabet + 1 is always illegal
+    # Since this code cannot occur from symbol encoding
+    # it can be later used to check for illegal symbols
+    cdef uint8 illegal_code = alphabet.shape[0]
+    # An array based map that maps from symbol to code
+    # Since the maximum value of a char is 256
+    # the size of the map is known at compile time
+    cdef uint8 sym_to_code[256]
+    # Initially fill the map with the illegal symbol
+    # Consequently, the map will later return the illegal symbol
+    # when indexed with a character that is not part of the alphabet
+    sym_to_code[:] = [illegal_code] * 256
+    # Then fill in entries for the symbols of the alphabet
+    cdef unsigned char symbol
+    for i, symbol in enumerate(alphabet):
+        sym_to_code[symbol] = i
+    
+    # Encode the symbols
+    code = np.empty(symbols.shape[0], dtype=np.uint8)
+    cdef uint8[:] code_view = code
+    cdef uint8 symbol_code
+    for i in range(symbols.shape[0]):
+        symbol_code = sym_to_code[symbols[i]]
+        # Check if the symbols is valid
+        if symbol_code == illegal_code:
+            illegal_symbol = chr(symbols[i])
+            # Local import to avoid circular imports
+            from .alphabet import AlphabetError
+            raise AlphabetError(
+                f"Symbol {repr(illegal_symbol)} is not in the alphabet"
+            )
+        code_view[i] = symbol_code
+
+    return code
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+def decode_to_chars(const unsigned char[:] alphabet not None,
+                    const uint8[:] code not None):
+    """
+    Decode an array of symbol codes into an array of symbols.
+
+    Only works for symbols that are printable ASCII characters.
+
+    Parameters
+    ----------
+    alphabet : ndarray, shape=(n,), dtype="|S1"
+        The alphabet as array.
+        It is indexed via ASCII values and the corresponding values are
+        the symbol codes.
+    code : ndarray, shape=(n,), dtype="|S1"
+        The code to be decoded.
+    
+    Returns
+    -------
+    symbols : ndarray, dtype="|S1"
+        The resulting symbols (ASCII characters).
+    """
+    cdef int i
+    cdef int alphabet_length = alphabet.shape[0]
+    
+    symbols = np.empty(code.shape[0], dtype=np.ubyte)
+    cdef uint8[:] symbols_view = symbols
+    cdef uint8 symbol_code
+    for i in range(code.shape[0]):
+        symbol_code = code[i]
+        if symbol_code >= alphabet_length:
+            # Local import to avoid circular imports
+            from .alphabet import AlphabetError
+            raise AlphabetError(f"'{symbol_code:d}' is not a valid code")
+        symbols_view[i] = alphabet[symbol_code]
+    return symbols
+
+
+ctypedef fused CodeType1:
+    uint8
+    uint16
+    uint32
+    uint64
+ctypedef fused CodeType2:
+    uint8
+    uint16
+    uint32
+    uint64
+def map_sequence_code(CodeType2[:] mapping,
+                      CodeType1[:] in_code, CodeType2[:] out_code):
+    """
+    Efficiently maps a sequence code into another alphabet using a
+    mapping.
+
+    Parameters
+    ----------
+    mapping : ndarray, dtype=int
+        Maps the input codes to output codes.
+    in_code : ndarray, shape=(n,), dtype=int
+        The symbol codes to be mapped.
+    out_code : ndarray, shape=(n,), dtype=int
+        An empty array, where the mapped symbols are stored.
+        This is a parameter instead of the return value in order to
+        choose the correct integer type.
+    """
+    cdef int64 i
+    if in_code.shape[0] != out_code.shape[0]:
+        raise ValueError(
+            f"Input sequence code has length {in_code.shape[0]}, "
+            f"but output sequence code has length {out_code.shape[0]}"
+        )
+    for i in range(in_code.shape[0]):
+        out_code[i] = mapping[in_code[i]]

biotite/sequence/codon.py

@@ -0,0 +1,476 @@
+# 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__ = ["CodonTable"]
+
+import copy
+from numbers import Integral
+from os.path import dirname, join, realpath
+import numpy as np
+from biotite.sequence.seqtypes import NucleotideSequence, ProteinSequence
+
+# Abbreviations
+_NUC_ALPH = NucleotideSequence.alphabet_unamb
+_PROT_ALPH = ProteinSequence.alphabet
+
+# Multiplier array that converts a codon in code representation
+# into a unique integer
+_radix = len(_NUC_ALPH)
+_radix_multiplier = np.array([_radix**n for n in (2, 1, 0)], dtype=int)
+
+
+class CodonTable(object):
+    """
+    A :class:`CodonTable` maps a codon (sequence of 3 nucleotides) to an
+    amino acid.
+    It also defines start codons. A :class:`CodonTable`
+    takes/outputs either the symbols or code of the codon/amino acid.
+
+    Furthermore, this class is able to give a list of codons that
+    corresponds to a given amino acid.
+
+    The :func:`load()` method allows loading of NCBI codon tables.
+
+    Objects of this class are immutable.
+
+    Parameters
+    ----------
+    codon_dict : dict of (str -> str)
+        A dictionary that maps codons to amino acids. The keys must be
+        strings of length 3 and the values strings of length 1
+        (all upper case).
+        The dictionary must provide entries for all 64 possible codons.
+    starts : iterable object of str
+        The start codons. Each entry must be a string of length 3
+        (all upper case).
+
+    Examples
+    --------
+
+    Get the amino acid coded by a given codon (symbol and code):
+
+    >>> table = CodonTable.default_table()
+    >>> print(table["ATG"])
+    M
+    >>> print(table[(1,2,3)])
+    14
+
+    Get the codons coding for a given amino acid (symbol and code):
+
+    >>> table = CodonTable.default_table()
+    >>> print(table["M"])
+    ('ATG',)
+    >>> print(table[14])
+    ((0, 2, 0), (0, 2, 2), (1, 2, 0), (1, 2, 1), (1, 2, 2), (1, 2, 3))
+    """
+
+    # For efficient mapping of codon codes to amino acid codes,
+    # especially in in the 'map_codon_codes()' function, the class
+    # maps each possible codon into a unique number using a radix based
+    # approach.
+    # For example the codon (3,1,2) would be represented as
+    # 3*16 + 1*4 + 2**1 = 53
+
+    # file for builtin codon tables from NCBI
+    _table_file = join(dirname(realpath(__file__)), "codon_tables.txt")
+
+    def __init__(self, codon_dict, starts):
+        # Check if 'starts' is iterable object of length 3 string
+        for start in starts:
+            if not isinstance(start, str) or len(start) != 3:
+                raise ValueError(f"Invalid codon '{start}' as start codon")
+        # Internally store codons as single unique numbers
+        start_codon_codes = np.array(
+            [_NUC_ALPH.encode_multiple(start) for start in starts], dtype=int
+        )
+        self._starts = CodonTable._to_number(start_codon_codes)
+        # Use -1 as error code
+        # The array uses the number representation of codons as index
+        # and stores the corresponding symbol codes for amino acids
+        self._codons = np.full(_radix**3, -1, dtype=int)
+        for key, value in codon_dict.items():
+            codon_code = _NUC_ALPH.encode_multiple(key)
+            codon_number = CodonTable._to_number(codon_code)
+            aa_code = _PROT_ALPH.encode(value)
+            self._codons[codon_number] = aa_code
+        if (self._codons == -1).any():
+            # Find the missing codon
+            missing_index = np.where(self._codons == -1)[0][0]
+            codon_code = CodonTable._to_codon(missing_index)
+            codon = _NUC_ALPH.decode_multiple(codon_code)
+            codon_str = "".join(codon)
+            raise ValueError(f"Codon dictionary does not contain codon '{codon_str}'")
+
+    def __repr__(self):
+        """Represent CodonTable as a string for debugging."""
+        return f"CodonTable({self.codon_dict()}, {self.start_codons()})"
+
+    def __eq__(self, item):
+        if not isinstance(item, CodonTable):
+            return False
+        if self.codon_dict() != item.codon_dict():
+            return False
+        if self.start_codons() != item.start_codons():
+            return False
+        return True
+
+    def __ne__(self, item):
+        return not self == item
+
+    def __getitem__(self, item):
+        if isinstance(item, str):
+            if len(item) == 1:
+                # Amino acid -> return possible codons
+                aa_code = _PROT_ALPH.encode(item)
+                codon_numbers = np.where(self._codons == aa_code)[0]
+                codon_codes = CodonTable._to_codon(codon_numbers)
+                codons = tuple(
+                    [
+                        "".join(_NUC_ALPH.decode_multiple(codon_code))
+                        for codon_code in codon_codes
+                    ]
+                )
+                return codons
+            elif len(item) == 3:
+                # Codon -> return corresponding amino acid
+                codon_code = _NUC_ALPH.encode_multiple(item)
+                codon_number = CodonTable._to_number(codon_code)
+                aa_code = self._codons[codon_number]
+                aa = _PROT_ALPH.decode(aa_code)
+                return aa
+            else:
+                raise ValueError(f"'{item}' is an invalid index")
+        elif isinstance(item, int):
+            # Code for amino acid -> return possible codon codes
+            codon_numbers = np.where(self._codons == item)[0]
+            codon_codes = tuple(
+                [tuple(code.tolist()) for code in CodonTable._to_codon(codon_numbers)]
+            )
+            return codon_codes
+        else:
+            # Code for codon as any iterable object
+            # Code for codon -> return corresponding amino acid codes
+            if len(item) != 3:
+                raise ValueError(f"{item} is an invalid sequence code for a codon")
+            codon_number = CodonTable._to_number(item)
+            aa_code = self._codons[codon_number]
+            return aa_code
+
+    def map_codon_codes(self, codon_codes):
+        """
+        Efficiently map multiple codons to the corresponding amino
+        acids.
+
+        Parameters
+        ----------
+        codon_codes : ndarray, dtype=int, shape=(n,3)
+            The codons to be translated into amino acids.
+            The codons are given as symbol codes.
+            *n* is the amount of codons.
+
+        Returns
+        -------
+        aa_codes : ndarray, dtype=int, shape=(n,)
+            The amino acids as symbol codes.
+
+        Examples
+        --------
+        >>> dna = NucleotideSequence("ATGGTTTAA")
+        >>> sequence_code = dna.code
+        >>> print(sequence_code)
+        [0 3 2 2 3 3 3 0 0]
+        >>> # Reshape to get codons
+        >>> codon_codes = sequence_code.reshape(-1, 3)
+        >>> print(codon_codes)
+        [[0 3 2]
+         [2 3 3]
+         [3 0 0]]
+        >>> # Map to amino acids
+        >>> aa_codes = CodonTable.default_table().map_codon_codes(codon_codes)
+        >>> print(aa_codes)
+        [10 17 23]
+        >>> # Put into a protein sequence
+        >>> protein = ProteinSequence()
+        >>> protein.code = aa_codes
+        >>> print(protein)
+        MV*
+        """
+        if codon_codes.shape[-1] != 3:
+            raise ValueError(
+                f"Codons must be length 3, "
+                f"but size of last dimension is {codon_codes.shape[-1]}"
+            )
+        codon_numbers = CodonTable._to_number(codon_codes)
+        aa_codes = self._codons[codon_numbers]
+        return aa_codes
+
+    def codon_dict(self, code=False):
+        """
+        Get the codon to amino acid mappings dictionary.
+
+        Parameters
+        ----------
+        code : bool
+            If true, the dictionary contains keys and values as code.
+            Otherwise, the dictionary contains strings for codons and
+            amino acid.
+
+        Returns
+        -------
+        codon_dict : dict
+            The dictionary mapping codons to amino acids.
+        """
+        if code:
+            return {
+                tuple(CodonTable._to_codon(codon_number)): aa_code
+                for codon_number, aa_code in enumerate(self._codons)
+            }
+        else:
+            return {
+                "".join(_NUC_ALPH.decode_multiple(codon_code)): _PROT_ALPH.decode(
+                    aa_code
+                )
+                for codon_code, aa_code in self.codon_dict(code=True).items()
+            }
+
+    def is_start_codon(self, codon_codes):
+        codon_numbers = CodonTable._to_number(codon_codes)
+        return np.isin(codon_numbers, self._starts)
+
+    def start_codons(self, code=False):
+        """
+        Get the start codons of the codon table.
+
+        Parameters
+        ----------
+        code : bool
+            If true, the code will be returned instead of strings.
+
+        Returns
+        -------
+        start_codons : tuple
+            The start codons. Contains strings or tuples, depending on
+            the `code` parameter.
+        """
+        if code:
+            return tuple(
+                [
+                    tuple(CodonTable._to_codon(codon_number))
+                    for codon_number in self._starts
+                ]
+            )
+        else:
+            return tuple(
+                [
+                    "".join(_NUC_ALPH.decode_multiple(codon_code))
+                    for codon_code in self.start_codons(code=True)
+                ]
+            )
+
+    def with_start_codons(self, starts):
+        """
+        Create an new :class:`CodonTable` with the same codon mappings,
+        but changed start codons.
+
+        Parameters
+        ----------
+        starts : iterable object of str
+            The new start codons.
+
+        Returns
+        -------
+        new_table : CodonTable
+            The codon table with the new start codons.
+        """
+        # Copy this table and replace the start codons
+        new_table = copy.deepcopy(self)
+        start_codon_codes = np.array(
+            [_NUC_ALPH.encode_multiple(start) for start in starts], dtype=int
+        )
+        new_table._starts = CodonTable._to_number(start_codon_codes)
+        return new_table
+
+    def with_codon_mappings(self, codon_dict):
+        """
+        Create an new :class:`CodonTable` with partially changed codon
+        mappings.
+
+        Parameters
+        ----------
+        codon_dict : dict of (str -> str)
+            The changed codon mappings.
+
+        Returns
+        -------
+        new_table : CodonTable
+            The codon table with changed codon mappings.
+        """
+        # Copy this table and replace the codon
+        new_table = copy.deepcopy(self)
+        for key, value in codon_dict.items():
+            codon_code = _NUC_ALPH.encode_multiple(key)
+            codon_number = CodonTable._to_number(codon_code)
+            aa_code = _PROT_ALPH.encode(value)
+            new_table._codons[codon_number] = aa_code
+        return new_table
+
+    def __str__(self):
+        string = ""
+        # ['A', 'C', 'G', 'T']
+        bases = _NUC_ALPH.get_symbols()
+        for b1 in bases:
+            for b2 in bases:
+                for b3 in bases:
+                    codon = b1 + b2 + b3
+                    string += codon + " " + self[codon]
+                    # Indicator for start codon
+                    codon_code = _NUC_ALPH.encode_multiple(codon)
+                    if CodonTable._to_number(codon_code) in self._starts:
+                        string += " i "
+                    else:
+                        string += "   "
+                    # Add space for next codon
+                    string += " " * 3
+                # Remove terminal space
+                string = string[:-6]
+                # Jump to next line
+                string += "\n"
+            # Add empty line
+            string += "\n"
+        # Remove the two terminal new lines
+        string = string[:-2]
+        return string
+
+    @staticmethod
+    def _to_number(codons):
+        if not isinstance(codons, np.ndarray):
+            codons = np.array(list(codons), dtype=int)
+        return np.sum(_radix_multiplier * codons, axis=-1)
+
+    @staticmethod
+    def _to_codon(numbers):
+        if isinstance(numbers, Integral):
+            # Only a single number
+            return CodonTable._to_codon(np.array([numbers]))[0]
+        if not isinstance(numbers, np.ndarray):
+            numbers = np.array(list(numbers), dtype=int)
+        codons = np.zeros(numbers.shape + (3,), dtype=int)
+        for n in (2, 1, 0):
+            val = _radix**n
+            digit = numbers // val
+            codons[..., -(n + 1)] = digit
+            numbers = numbers - digit * val
+        return codons
+
+    @staticmethod
+    def load(table_name):
+        """
+        Load a NCBI codon table.
+
+        Parameters
+        ----------
+        table_name : str or int
+            If a string is given, it is interpreted as official NCBI
+            codon table name (e.g. "Vertebrate Mitochondrial").
+            An integer is interpreted as NCBI codon table ID.
+
+        Returns
+        -------
+        table : CodonTable
+            The NCBI codon table.
+        """
+        # Loads codon tables from codon_tables.txt
+        with open(CodonTable._table_file, "r") as f:
+            lines = f.read().split("\n")
+
+        # Extract data for codon table from file
+        table_found = False
+        aa = None
+        init = None
+        base1 = None
+        base2 = None
+        base3 = None
+        for line in lines:
+            if not line:
+                table_found = False
+            if isinstance(table_name, Integral) and line.startswith("id"):
+                # remove identifier 'id'
+                if table_name == int(line[2:]):
+                    table_found = True
+            elif isinstance(table_name, str) and line.startswith("name"):
+                # Get list of table names from lines
+                # (separated with ';')
+                # remove identifier 'name'
+                names = [name.strip() for name in line[4:].split(";")]
+                if table_name in names:
+                    table_found = True
+            if table_found:
+                if line.startswith("AA"):
+                    # Remove identifier
+                    aa = line[5:].strip()
+                elif line.startswith("Init"):
+                    init = line[5:].strip()
+                elif line.startswith("Base1"):
+                    base1 = line[5:].strip()
+                elif line.startswith("Base2"):
+                    base2 = line[5:].strip()
+                elif line.startswith("Base3"):
+                    base3 = line[5:].strip()
+
+        # Create codon table from data
+        if (
+            aa is not None
+            and init is not None
+            and base1 is not None
+            and base2 is not None
+            and base3 is not None
+        ):
+            symbol_dict = {}
+            starts = []
+            # aa, init and baseX all have the same length
+            for i in range(len(aa)):
+                codon = base1[i] + base2[i] + base3[i]
+                if init[i] == "i":
+                    starts.append(codon)
+                symbol_dict[codon] = aa[i]
+            return CodonTable(symbol_dict, starts)
+        else:
+            raise ValueError(f"Codon table '{table_name}' was not found")
+
+    @staticmethod
+    def table_names():
+        """
+        The possible codon table names for :func:`load()`.
+
+        Returns
+        -------
+        names : list of str
+            List of valid codon table names.
+        """
+        with open(CodonTable._table_file, "r") as f:
+            lines = f.read().split("\n")
+        names = []
+        for line in lines:
+            if line.startswith("name"):
+                names.extend([name.strip() for name in line[4:].split(";")])
+        return names
+
+    @staticmethod
+    def default_table():
+        """
+        The default codon table.
+        The table is equal to the NCBI "Standard" codon table,
+        with the difference that only "ATG" is a start codon.
+
+        Returns
+        -------
+        table : CodonTable
+            The default codon table.
+        """
+        return _default_table
+
+
+_default_table = CodonTable.load("Standard").with_start_codons(["ATG"])