biotite 0.41.1__cp312-cp312-win_amd64.whl → 1.0.0__cp312-cp312-win_amd64.whl

biotite/sequence/align/cigar.py

@@ -8,13 +8,14 @@ __all__ = ["CigarOp", "read_alignment_from_cigar", "write_alignment_to_cigar"]
 
 import enum
 import numpy as np
-from .alignment import Alignment, get_codes
+from biotite.sequence.align.alignment import Alignment, get_codes
 
 
 class CigarOp(enum.IntEnum):
     """
     An enum for the different CIGAR operations.
     """
+
     MATCH = 0
     INSERTION = 1
     DELETION = 2
@@ -46,23 +47,23 @@ class CigarOp(enum.IntEnum):
     def to_cigar_symbol(self):
         return _op_to_str[self]
 
+
 _str_to_op = {
-        "M" : CigarOp.MATCH,
-        "I" : CigarOp.INSERTION,
-        "D" : CigarOp.DELETION,
-        "N" : CigarOp.INTRON,
-        "S" : CigarOp.SOFT_CLIP,
-        "H" : CigarOp.HARD_CLIP,
-        "P" : CigarOp.PADDING,
-        "=" : CigarOp.EQUAL,
-        "X" : CigarOp.DIFFERENT,
-        "B" : CigarOp.BACK
-    }
+    "M": CigarOp.MATCH,
+    "I": CigarOp.INSERTION,
+    "D": CigarOp.DELETION,
+    "N": CigarOp.INTRON,
+    "S": CigarOp.SOFT_CLIP,
+    "H": CigarOp.HARD_CLIP,
+    "P": CigarOp.PADDING,
+    "=": CigarOp.EQUAL,
+    "X": CigarOp.DIFFERENT,
+    "B": CigarOp.BACK,
+}
 _op_to_str = {v: k for k, v in _str_to_op.items()}
 
 
-def read_alignment_from_cigar(cigar, position,
-                              reference_sequence, segment_sequence):
+def read_alignment_from_cigar(cigar, position, reference_sequence, segment_sequence):
     """
     Create an :class:`Alignment` from a CIGAR string.
 
@@ -147,20 +148,16 @@ def read_alignment_from_cigar(cigar, position,
     else:
         operations = np.asarray(cigar, dtype=int)
         if operations.ndim != 2:
-            raise ValueError(
-                "Expected array with shape (n,2)"
-            )
+            raise ValueError("Expected array with shape (n,2)")
         if operations.shape[1] != 2:
-            raise ValueError(
-                "Expected (operation, length) pairs"
-            )
+            raise ValueError("Expected (operation, length) pairs")
 
     if len(operations) == 0:
         return Alignment(
             [reference_sequence, segment_sequence], np.zeros((0, 2), dtype=int)
         )
 
-    trace = np.zeros((np.sum(operations[:,1]), 2), dtype=int)
+    trace = np.zeros((np.sum(operations[:, 1]), 2), dtype=int)
     clip_mask = np.ones(trace.shape[0], dtype=bool)
 
     i = 0
@@ -187,19 +184,23 @@ def read_alignment_from_cigar(cigar, position,
         elif op == CigarOp.HARD_CLIP:
             clip_mask[i : i + length] = False
         else:
-            raise ValueError(
-                f"CIGAR operation {op} is not implemented"
-            )
+            raise ValueError(f"CIGAR operation {op} is not implemented")
         i += length
     # Remove clipped positions
     trace = trace[clip_mask]
     return Alignment([reference_sequence, segment_sequence], trace)
 
 
-def write_alignment_to_cigar(alignment, reference_index=0, segment_index=1,
-                             introns=(), distinguish_matches=False,
-                             hard_clip=False, include_terminal_gaps=False,
-                             as_string=True):
+def write_alignment_to_cigar(
+    alignment,
+    reference_index=0,
+    segment_index=1,
+    introns=(),
+    distinguish_matches=False,
+    hard_clip=False,
+    include_terminal_gaps=False,
+    as_string=True,
+):
     """
     Convert an :class:`Alignment` into a CIGAR string.
 
@@ -293,10 +294,10 @@ def write_alignment_to_cigar(alignment, reference_index=0, segment_index=1,
 
     >>> op_tuples = write_alignment_to_cigar(semiglobal_alignment, as_string=False)
     >>> for op, length in op_tuples:
-    ...     print(CigarOp(op), length)
-    CigarOp.MATCH 9
-    CigarOp.DELETION 2
-    CigarOp.MATCH 12
+    ...     print(CigarOp(op).name, length)
+    MATCH 9
+    DELETION 2
+    MATCH 12
     """
     if not include_terminal_gaps:
         alignment = _remove_terminal_segment_gaps(alignment, segment_index)
@@ -305,8 +306,8 @@ def write_alignment_to_cigar(alignment, reference_index=0, segment_index=1,
     seg_trace = alignment.trace[:, segment_index]
     operations = np.full(alignment.trace.shape[0], CigarOp.MATCH, dtype=int)
 
-    insertion_mask = (ref_trace == -1)
-    deletion_mask = (seg_trace == -1)
+    insertion_mask = ref_trace == -1
+    deletion_mask = seg_trace == -1
     if np.any(insertion_mask & deletion_mask):
         raise ValueError(
             "Alignment contains insertion and deletion at the same position"
@@ -318,35 +319,27 @@ def write_alignment_to_cigar(alignment, reference_index=0, segment_index=1,
         intron_mask = np.zeros(operations.shape[0], dtype=bool)
         for start, stop in introns:
             if start >= stop:
-                raise ValueError(
-                    "Intron start must be smaller than intron stop"
-                )
+                raise ValueError("Intron start must be smaller than intron stop")
             if start < 0:
-                raise ValueError(
-                    "Intron start must not be negative"
-                )
+                raise ValueError("Intron start must not be negative")
             intron_mask[(ref_trace >= start) & (ref_trace < stop)] = True
         if np.any(intron_mask & ~deletion_mask):
-            raise ValueError(
-                "Introns must be within gaps in the reference sequence"
-            )
+            raise ValueError("Introns must be within gaps in the reference sequence")
         operations[intron_mask] = CigarOp.INTRON
 
     if distinguish_matches:
         symbol_codes = get_codes(alignment)
         ref_codes = symbol_codes[reference_index, :]
         seg_codes = symbol_codes[segment_index, :]
-        equal_mask = (ref_codes == seg_codes)
-        match_mask = (operations == CigarOp.MATCH)
+        equal_mask = ref_codes == seg_codes
+        match_mask = operations == CigarOp.MATCH
         operations[equal_mask & match_mask] = CigarOp.EQUAL
         operations[~equal_mask & match_mask] = CigarOp.DIFFERENT
 
     op_tuples = _aggregate_consecutive(operations)
 
     clip_op = CigarOp.HARD_CLIP if hard_clip else CigarOp.SOFT_CLIP
-    start_clip_length, end_clip_length = _find_clipped_bases(
-        alignment, segment_index
-    )
+    start_clip_length, end_clip_length = _find_clipped_bases(alignment, segment_index)
     if start_clip_length != 0:
         start_clip = [(clip_op, start_clip_length)]
     else:
@@ -386,9 +379,7 @@ def _find_clipped_bases(alignment, segment_index):
     # all previous bases are clipped...
     start_clip_length = seg_trace[0]
     # ...and the same applies for the last base
-    end_clip_length = (
-        len(alignment.sequences[segment_index]) - seg_trace[-1] - 1
-    )
+    end_clip_length = len(alignment.sequences[segment_index]) - seg_trace[-1] - 1
     return start_clip_length, end_clip_length
 
 
@@ -431,4 +422,4 @@ def _op_tuples_from_cigar(cigar):
             op = CigarOp.from_cigar_symbol(char)
             op_tuples.append((op, count))
             count = ""
-    return np.array(op_tuples, dtype=int)
+    return np.array(op_tuples, dtype=int)

biotite/sequence/align/kmeralphabet.pyx

@@ -33,7 +33,7 @@ class KmerAlphabet(Alphabet):
 
     This type of alphabet uses *k-mers* as symbols, i.e. all
     combinations of *k* symbols from its *base alphabet*.
-    
+
     It's primary use is its :meth:`create_kmers()` method, that iterates
     over all overlapping *k-mers* in a :class:`Sequence` and encodes
     each one into its corresponding *k-mer* symbol code
@@ -68,7 +68,7 @@ class KmerAlphabet(Alphabet):
         integers, that indicate the *informative* positions.
         For a continuous *k-mer* the `spacing` would be
         ``[0, 1, 2,...]``.
-    
+
     Attributes
     ----------
     base_alphabet : Alphabet
@@ -79,7 +79,7 @@ class KmerAlphabet(Alphabet):
     spacing : None or ndarray, dtype=int
         The *k-mer* model in array form, if spaced *k-mers* are used,
         ``None`` otherwise.
-    
+
     Notes
     -----
     The symbol code for a *k-mer* :math:`s` calculates as
@@ -94,7 +94,7 @@ class KmerAlphabet(Alphabet):
 
     References
     ----------
-    
+
     .. footbibliography::
 
     Examples
@@ -103,11 +103,11 @@ class KmerAlphabet(Alphabet):
 
     >>> base_alphabet = NucleotideSequence.unambiguous_alphabet()
     >>> print(base_alphabet.get_symbols())
-    ['A', 'C', 'G', 'T']
+    ('A', 'C', 'G', 'T')
     >>> kmer_alphabet = KmerAlphabet(base_alphabet, 2)
     >>> print(kmer_alphabet.get_symbols())
-    ['AA', 'AC', 'AG', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA', 'TC', 'TG', 'TT']
-    
+    ('AA', 'AC', 'AG', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA', 'TC', 'TG', 'TT')
+
     Encode and decode *k-mers*:
 
     >>> print(kmer_alphabet.encode("TC"))
@@ -127,7 +127,7 @@ class KmerAlphabet(Alphabet):
     [3 1]
 
     Encode all overlapping continuous k-mers of a sequence:
-    
+
     >>> sequence = NucleotideSequence("ATTGCT")
     >>> kmer_codes = kmer_alphabet.create_kmers(sequence.code)
     >>> print(kmer_codes)
@@ -146,7 +146,7 @@ class KmerAlphabet(Alphabet):
     >>> print([s[0] + s[1] + "_" + s[2] for s in strings])
     ['BI_T', 'IQ_I', 'QT_T', 'TI_E']
     """
-    
+
     def __init__(self, base_alphabet, k, spacing=None):
         if not isinstance(base_alphabet, Alphabet):
             raise TypeError(
@@ -157,7 +157,7 @@ class KmerAlphabet(Alphabet):
             raise ValueError("k must be at least 2")
         self._base_alph = base_alphabet
         self._k = k
-        
+
         base_alph_len = len(self._base_alph)
         self._radix_multiplier = np.array(
             [base_alph_len**n for n in reversed(range(0, self._k))],
@@ -166,10 +166,10 @@ class KmerAlphabet(Alphabet):
 
         if spacing is None:
             self._spacing = None
-        
+
         elif isinstance(spacing, str):
             self._spacing = _to_array_form(spacing)
-        
+
         else:
             self._spacing = np.array(spacing, dtype=np.int64)
             self._spacing.sort()
@@ -181,13 +181,13 @@ class KmerAlphabet(Alphabet):
                 raise ValueError(
                     "Spacing model contains duplicate values"
                 )
-        
+
         if spacing is not None and len(self._spacing) != self._k:
             raise ValueError(
                 f"Expected {self._k} informative positions, "
                 f"but got {len(self._spacing)} positions in spacing"
             )
-    
+
 
     @property
     def base_alphabet(self):
@@ -196,11 +196,11 @@ class KmerAlphabet(Alphabet):
     @property
     def k(self):
         return self._k
-    
+
     @property
     def spacing(self):
         return None if self._spacing is None else self._spacing.copy()
-    
+
 
     def get_symbols(self):
         """
@@ -210,10 +210,10 @@ class KmerAlphabet(Alphabet):
 
         Returns
         -------
-        symbols : list
-            A list of all *k-mer* symbols, i.e. all possible
+        symbols : tuple
+            A tuple of all *k-mer* symbols, i.e. all possible
             combinations of *k* symbols from its *base alphabet*.
-        
+
         Notes
         -----
         In contrast the base :class:`Alphabet` and
@@ -224,10 +224,10 @@ class KmerAlphabet(Alphabet):
         to be created first.
         """
         if isinstance(self._base_alph, LetterAlphabet):
-            return ["".join(self.decode(code)) for code in range(len(self))]
+            return tuple(["".join(self.decode(code)) for code in range(len(self))])
         else:
-            return [list(self.decode(code)) for code in range(len(self))]
-    
+            return tuple([list(self.decode(code)) for code in range(len(self))])
+
 
     def extends(self, alphabet):
         # A KmerAlphabet cannot really extend another KmerAlphabet:
@@ -237,15 +237,15 @@ class KmerAlphabet(Alphabet):
         # A KmerAlphabet can only 'extend' another KmerAlphabet,
         # if the two alphabets are equal
         return alphabet == self
-    
+
 
     def encode(self, symbol):
         return self.fuse(self._base_alph.encode_multiple(symbol))
-    
+
 
     def decode(self, code):
         return self._base_alph.decode_multiple(self.split(code))
-    
+
 
     def fuse(self, codes):
         """
@@ -261,7 +261,7 @@ class KmerAlphabet(Alphabet):
         ----------
         codes : ndarray, dtype=int, shape=(k,) or shape=(n,k)
             The symbol codes from the base alphabet to be fused.
-        
+
         Returns
         -------
         kmer_codes : int or ndarray, dtype=np.int64, shape=(n,)
@@ -292,13 +292,13 @@ class KmerAlphabet(Alphabet):
             )
         if np.any(codes > len(self._base_alph)):
             raise AlphabetError("Given k-mer(s) contains invalid symbol code")
-        
+
         orig_shape = codes.shape
         codes = np.atleast_2d(codes)
         kmer_code = np.sum(self._radix_multiplier * codes, axis=-1)
         # The last dimension is removed since it collpased in np.sum
         return kmer_code.reshape(orig_shape[:-1])
-    
+
     def split(self, kmer_code):
         """
         split(kmer_code)
@@ -313,7 +313,7 @@ class KmerAlphabet(Alphabet):
         ----------
         kmer_code : int or ndarray, dtype=int, shape=(n,)
             The *k-mer* code(s).
-        
+
         Returns
         -------
         codes : ndarray, dtype=np.uint64, shape=(k,) or shape=(n,k)
@@ -341,13 +341,13 @@ class KmerAlphabet(Alphabet):
             raise AlphabetError(
                 f"Given k-mer symbol code is invalid for this alphabet"
             )
-        
+
         orig_shape = np.shape(kmer_code)
         split_codes = self._split(
             np.atleast_1d(kmer_code).astype(np.int64, copy=False)
         )
         return split_codes.reshape(orig_shape + (self._k,))
-    
+
     @cython.boundscheck(False)
     @cython.wraparound(False)
     @cython.cdivision(True)
@@ -360,7 +360,7 @@ class KmerAlphabet(Alphabet):
         cdef uint64[:,:] split_codes = np.empty(
             (codes.shape[0], self._k), dtype=np.uint64
         )
-        
+
         cdef int k = self._k
         for i in range(codes.shape[0]):
             code = codes[i]
@@ -369,9 +369,9 @@ class KmerAlphabet(Alphabet):
                 symbol_code = code // val
                 split_codes[i,n] = symbol_code
                 code -= symbol_code * val
-        
+
         return np.asarray(split_codes)
-    
+
 
     def kmer_array_length(self, int64 length):
         """
@@ -385,7 +385,7 @@ class KmerAlphabet(Alphabet):
         ----------
         length : int
             The length of the hypothetical sequence
-        
+
         Returns
         -------
         kmer_length : int
@@ -400,7 +400,7 @@ class KmerAlphabet(Alphabet):
             spacing = self._spacing
             max_offset = self._spacing[len(spacing)-1] + 1
             return length - max_offset + 1
-    
+
 
     def create_kmers(self, seq_code):
         """
@@ -418,7 +418,7 @@ class KmerAlphabet(Alphabet):
         -------
         kmer_codes : ndarray, dtype=int64
             The symbol codes for the *k-mers*.
-        
+
         Examples
         --------
 
@@ -435,7 +435,7 @@ class KmerAlphabet(Alphabet):
             return self._create_continuous_kmers(seq_code)
         else:
             return self._create_spaced_kmers(seq_code)
-    
+
     @cython.boundscheck(False)
     @cython.wraparound(False)
     def _create_continuous_kmers(self, CodeType[:] seq_code not None):
@@ -460,7 +460,7 @@ class KmerAlphabet(Alphabet):
         cdef int64[:] kmers = np.empty(
             self.kmer_array_length(len(seq_code)), dtype=np.int64
         )
-        
+
         cdef CodeType code
         cdef int64 kmer, prev_kmer
         # Compute first k-mer using naive approach
@@ -471,7 +471,7 @@ class KmerAlphabet(Alphabet):
                 raise AlphabetError(f"Symbol code {code} is out of range")
             kmer += radix_multiplier[i] * code
         kmers[0] = kmer
-        
+
         # Compute all following k-mers from the previous one
         prev_kmer = kmer
         for i in range(1, kmers.shape[0]):
@@ -481,7 +481,7 @@ class KmerAlphabet(Alphabet):
             kmer = (
                 (
                     # Remove first symbol
-                    (prev_kmer - seq_code[i - 1] * end_radix_multiplier)   
+                    (prev_kmer - seq_code[i - 1] * end_radix_multiplier)
                     # Shift k-mer to left
                     * alphabet_length
                 )
@@ -490,9 +490,9 @@ class KmerAlphabet(Alphabet):
             )
             kmers[i] = kmer
             prev_kmer = kmer
-        
+
         return np.asarray(kmers)
-    
+
     @cython.boundscheck(False)
     @cython.wraparound(False)
     def _create_spaced_kmers(self, CodeType[:] seq_code not None):
@@ -515,7 +515,7 @@ class KmerAlphabet(Alphabet):
         cdef int64[:] kmers = np.empty(
             self.kmer_array_length(len(seq_code)), dtype=np.int64
         )
-        
+
         cdef CodeType code
         cdef int64 kmer
         cdef int64 offset
@@ -528,18 +528,18 @@ class KmerAlphabet(Alphabet):
                     raise AlphabetError(f"Symbol code {code} is out of range")
                 kmer += radix_multiplier[j] * code
             kmers[i] = kmer
-        
+
         return np.asarray(kmers)
-    
+
 
     def __str__(self):
         return str(self.get_symbols())
-    
+
 
     def __repr__(self):
         return f"KmerAlphabet({repr(self._base_alph)}, " \
                f"{self._k}, {repr(self._spacing)})"
-    
+
 
     def __eq__(self, item):
         if item is self:
@@ -550,15 +550,19 @@ class KmerAlphabet(Alphabet):
             return False
         if self._k != item._k:
             return False
-        
+
         if self._spacing is None:
             if item._spacing is not None:
                 return False
         elif np.any(self._spacing != item._spacing):
             return False
-        
+
         return True
-    
+
+
+    def __hash__(self):
+        return hash((self._base_alph, self._k, tuple(self._spacing.tolist())))
+
 
     def __len__(self):
         return int(len(self._base_alph) ** self._k)

biotite/sequence/align/kmertable.pyx

@@ -1352,7 +1352,8 @@ cdef class KmerTable:
 
 
     def __iter__(self):
-        return iter(self.get_kmers())
+        for kmer in self.get_kmers():
+            yield kmer.item()
 
 
     def __reversed__(self):
@@ -3394,7 +3395,7 @@ def _to_string(table):
         else:
             symbols = str(tuple(symbols))
         line = symbols + ": " + ", ".join(
-            [str(tuple(pos)) for pos in table[kmer]]
+            [str((ref_id.item(), pos.item())) for ref_id, pos in table[kmer]]
         )
         lines.append(line)
     return "\n".join(lines)