biotite 0.41.2__cp312-cp312-win_amd64.whl → 1.0.0__cp312-cp312-win_amd64.whl

biotite/sequence/align/selector.pyx

@@ -10,10 +10,8 @@ __all__ = ["MinimizerSelector", "SyncmerSelector", "CachedSyncmerSelector",
 cimport cython
 cimport numpy as np
 
-from numbers import Integral
 import numpy as np
 from .kmeralphabet import KmerAlphabet
-from ..alphabet import AlphabetError
 
 
 ctypedef np.int64_t int64
@@ -21,7 +19,7 @@ ctypedef np.uint32_t uint32
 
 
 # Obtained from 'np.iinfo(np.int64).max'
-DEF MAX_INT_64 = 9223372036854775807
+cdef int64 MAX_INT_64 = 9223372036854775807
 
 
 class MinimizerSelector:
@@ -54,7 +52,7 @@ class MinimizerSelector:
         This standard order is often the lexicographical order, which is
         known to yield suboptimal *density* in many cases
         :footcite:`Roberts2004`.
-    
+
     Attributes
     ----------
     kmer_alphabet : KmerAlphabet
@@ -73,7 +71,7 @@ class MinimizerSelector:
 
     References
     ----------
-    
+
     .. footbibliography::
 
     Examples
@@ -122,12 +120,12 @@ class MinimizerSelector:
         self._window = window
         self._kmer_alph = kmer_alphabet
         self._permutation = permutation
-    
+
 
     @property
     def kmer_alphabet(self):
         return self._kmer_alph
-    
+
     @property
     def window(self):
         return self._window
@@ -135,7 +133,7 @@ class MinimizerSelector:
     @property
     def permutation(self):
         return self._permutation
-    
+
 
     def select(self, sequence, bint alphabet_check=True):
         """
@@ -154,7 +152,7 @@ class MinimizerSelector:
             of the sequence and the alphabet of the
             :class:`MinimizerSelector`
             is not checked to gain additional performance.
-        
+
         Returns
         -------
         minimizer_indices : ndarray, dtype=np.uint32
@@ -162,7 +160,7 @@ class MinimizerSelector:
         minimizers : ndarray, dtype=np.int64
             The *k-mers* that are the selected minimizers, returned as
             *k-mer* code.
-        
+
         Notes
         -----
         Duplicate minimizers are omitted, i.e. if two windows have the
@@ -176,7 +174,7 @@ class MinimizerSelector:
                 )
         kmers = self._kmer_alph.create_kmers(sequence.code)
         return self.select_from_kmers(kmers)
-    
+
 
     def select_from_kmers(self, kmers):
         """
@@ -191,7 +189,7 @@ class MinimizerSelector:
             minimizers in.
             The *k-mer* codes correspond to the *k-mers* encoded by the
             given `kmer_alphabet`.
-        
+
         Returns
         -------
         minimizer_indices : ndarray, dtype=np.uint32
@@ -199,7 +197,7 @@ class MinimizerSelector:
             appears.
         minimizers : ndarray, dtype=np.int64
             The corresponding *k-mers* codes of the minimizers.
-        
+
         Notes
         -----
         Duplicate minimizers are omitted, i.e. if two windows have the
@@ -267,7 +265,7 @@ class SyncmerSelector:
         *k-mer*.
         By default, the minimum position needs to be at the start of the
         *k-mer*, which is termed *open syncmer*.
-    
+
     Attributes
     ----------
     alphabet : Alphabet
@@ -276,7 +274,7 @@ class SyncmerSelector:
         The :class:`KmerAlphabet` for *k* and *s*, respectively.
     permutation : Permutation
         The permutation.
-    
+
     See also
     --------
     CachedSyncmerSelector
@@ -291,7 +289,7 @@ class SyncmerSelector:
 
     References
     ----------
-    
+
     .. footbibliography::
 
     Examples
@@ -337,7 +335,7 @@ class SyncmerSelector:
         self._alphabet = alphabet
         self._kmer_alph = KmerAlphabet(alphabet, k)
         self._smer_alph = KmerAlphabet(alphabet, s)
-        
+
         self._permutation = permutation
 
         self._offset = np.asarray(offset, dtype=np.int64)
@@ -353,7 +351,7 @@ class SyncmerSelector:
             )
         if len(np.unique(self._offset)) != len(self._offset):
             raise ValueError("Offset must contain unique values")
-    
+
 
     @property
     def alphabet(self):
@@ -362,7 +360,7 @@ class SyncmerSelector:
     @property
     def kmer_alphabet(self):
         return self._kmer_alph
-    
+
     @property
     def smer_alphabet(self):
         return self._smer_alph
@@ -370,7 +368,7 @@ class SyncmerSelector:
     @property
     def permutation(self):
         return self._permutation
-    
+
 
     def select(self, sequence, bint alphabet_check=True):
         """
@@ -389,7 +387,7 @@ class SyncmerSelector:
             of the sequence and the alphabet of the
             :class:`SyncmerSelector`
             is not checked to gain additional performance.
-        
+
         Returns
         -------
         syncmer_indices : ndarray, dtype=np.uint32
@@ -428,7 +426,7 @@ class SyncmerSelector:
         relative_min_pos = min_pos - np.arange(len(kmers))
         syncmer_pos = self._filter_syncmer_pos(relative_min_pos)
         return syncmer_pos, kmers[syncmer_pos]
-    
+
 
     def select_from_kmers(self, kmers):
         """
@@ -442,7 +440,7 @@ class SyncmerSelector:
         ----------
         kmers : ndarray, dtype=np.int64
             The *k-mer* codes to select the syncmers from.
-        
+
         Returns
         -------
         syncmer_indices : ndarray, dtype=np.uint32
@@ -459,9 +457,9 @@ class SyncmerSelector:
         :class:`Sequence` objects.
         """
         cdef int64 i
-        
+
         symbol_codes_for_each_kmer = self._kmer_alph.split(kmers)
-        
+
         cdef int64[:] min_pos = np.zeros(
             len(symbol_codes_for_each_kmer), dtype=np.int64
         )
@@ -477,10 +475,10 @@ class SyncmerSelector:
                         f"sort keys for {len(smers)} s-mers"
                     )
             min_pos[i] = np.argmin(ordering)
-        
+
         syncmer_pos = self._filter_syncmer_pos(min_pos)
         return syncmer_pos, kmers[syncmer_pos]
-    
+
 
     def _filter_syncmer_pos(self, min_pos):
         """
@@ -538,7 +536,7 @@ class CachedSyncmerSelector(SyncmerSelector):
         *k-mer*.
         By default, the minimum position needs to be at the start of the
         *k-mer*, which is termed *open syncmer*.
-    
+
     Attributes
     ----------
     alphabet : Alphabet
@@ -547,7 +545,7 @@ class CachedSyncmerSelector(SyncmerSelector):
         The :class:`KmerAlphabet` for *k* and *s*, respectively.
     permutation : Permutation
         The permutation.
-    
+
     See also
     --------
     SyncmerSelector
@@ -562,7 +560,7 @@ class CachedSyncmerSelector(SyncmerSelector):
 
     References
     ----------
-    
+
     .. footbibliography::
 
     Examples
@@ -584,7 +582,7 @@ class CachedSyncmerSelector(SyncmerSelector):
     >>> print(["".join(kmer_alph.decode(kmer)) for kmer in syncmers])
     ['GGCAA', 'AAGTG', 'AGTGA', 'GTGAC']
     """
-    
+
     def __init__(self, alphabet, k, s, permutation=None, offset=(0,)):
         super().__init__(alphabet, k, s, permutation, offset)
         # Check for all possible *k-mers*, whether they are syncmers
@@ -593,7 +591,7 @@ class CachedSyncmerSelector(SyncmerSelector):
         # Convert the index array into a boolean mask
         self._syncmer_mask = np.zeros(len(self.kmer_alphabet), dtype=bool)
         self._syncmer_mask[syncmer_indices] = True
-    
+
 
     def select(self, sequence, bint alphabet_check=True):
         """
@@ -612,7 +610,7 @@ class CachedSyncmerSelector(SyncmerSelector):
             of the sequence and the alphabet of the
             :class:`CachedSyncmerSelector`
             is not checked to gain additional performance.
-        
+
         Returns
         -------
         syncmer_indices : ndarray, dtype=np.uint32
@@ -628,7 +626,7 @@ class CachedSyncmerSelector(SyncmerSelector):
                 )
         kmers = self.kmer_alphabet.create_kmers(sequence.code)
         return self.select_from_kmers(kmers)
-    
+
 
     def select_from_kmers(self, kmers):
         """
@@ -642,7 +640,7 @@ class CachedSyncmerSelector(SyncmerSelector):
         ----------
         kmers : ndarray, dtype=np.int64
             The *k-mer* codes to select the syncmers from.
-        
+
         Returns
         -------
         syncmer_indices : ndarray, dtype=np.uint32
@@ -660,7 +658,7 @@ class MincodeSelector:
 
     Selects the :math:`1/\text{compression}` *smallest* *k-mers* from
     :class:`KmerAlphabet`. :footcite:`Edgar2021`
-    
+
     '*Small*' refers to the lexicographical order, or alternatively a
     custom order if `permutation` is given.
     The *Mincode* approach tries to reduce the number of *k-mers* from a
@@ -682,7 +680,7 @@ class MincodeSelector:
         By default, the standard order of the :class:`KmerAlphabet` is
         used.
         This standard order is often the lexicographical order.
-    
+
     Attributes
     ----------
     kmer_alphabet : KmerAlphabet
@@ -695,10 +693,10 @@ class MincodeSelector:
         All *k-mers*, that are smaller than this value are selected.
     permutation : Permutation
         The permutation.
-    
+
     References
     ----------
-    
+
     .. footbibliography::
 
     Examples
@@ -735,12 +733,12 @@ class MincodeSelector:
             permutation_offset = permutation.min
             permutation_range = permutation.max - permutation.min + 1
         self._threshold = permutation_offset + permutation_range / compression
-    
+
 
     @property
     def kmer_alphabet(self):
         return self._kmer_alph
-    
+
     @property
     def compression(self):
         return self._compression
@@ -752,7 +750,7 @@ class MincodeSelector:
     @property
     def permutation(self):
         return self._permutation
-    
+
 
     def select(self, sequence, bint alphabet_check=True):
         """
@@ -771,7 +769,7 @@ class MincodeSelector:
             of the sequence and the alphabet of the
             :class:`MincodeSelector`
             is not checked to gain additional performance.
-        
+
         Returns
         -------
         mincode_indices : ndarray, dtype=np.uint32
@@ -786,7 +784,7 @@ class MincodeSelector:
                 )
         kmers = self._kmer_alph.create_kmers(sequence.code)
         return self.select_from_kmers(kmers)
-    
+
 
     def select_from_kmers(self, kmers):
         """
@@ -800,7 +798,7 @@ class MincodeSelector:
         ----------
         kmers : ndarray, dtype=np.int64
             The *k-mer* codes to select the *Mincode k-mers* from.
-        
+
         Returns
         -------
         mincode_indices : ndarray, dtype=np.uint32
@@ -820,7 +818,7 @@ class MincodeSelector:
 
         mincode_pos = ordering < self._threshold
         return mincode_pos, kmers[mincode_pos]
-    
+
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
@@ -835,7 +833,7 @@ def _minimize(int64[:] kmers, int64[:] ordering, uint32 window,
     instead of 'x - (window-1)/2' to 'x + (window-1)/2'.
     """
     cdef uint32 seq_i
-    
+
     cdef uint32 n_windows = kmers.shape[0] - (window - 1)
     # Pessimistic array allocation size
     # -> Expect that every window has a new minimizer
@@ -865,14 +863,14 @@ def _minimize(int64[:] kmers, int64[:] ordering, uint32 window,
         reverse_argcummin = reverse_argcummins[seq_i]
         forward_cummin = ordering[forward_argcummin]
         reverse_cummin = ordering[reverse_argcummin]
-        
+
         # At ties the leftmost position is taken,
         # which stems from the reverse pass
         if forward_cummin < reverse_cummin:
             combined_argcummin = forward_argcummin
         else:
             combined_argcummin = reverse_argcummin
-        
+
         # If the same minimizer position was observed before, the
         # duplicate is simply ignored, if 'include_duplicates' is false
         if include_duplicates or combined_argcummin != prev_argcummin:
@@ -899,7 +897,7 @@ cdef _chunk_wise_forward_argcummin(int64[:] values, uint32 chunk_size):
     cdef uint32 current_min_i = 0
     cdef int64 current_min, current_val
     cdef uint32[:] min_pos = np.empty(values.shape[0], dtype=np.uint32)
-    
+
     # Any actual value will be smaller than this placeholder
     current_min = MAX_INT_64
     for seq_i in range(values.shape[0]):
@@ -911,7 +909,7 @@ cdef _chunk_wise_forward_argcummin(int64[:] values, uint32 chunk_size):
             current_min_i = seq_i
             current_min = current_val
         min_pos[seq_i] = current_min_i
-    
+
     return min_pos
 
 @cython.boundscheck(False)
@@ -930,7 +928,7 @@ cdef _chunk_wise_reverse_argcummin(int64[:] values, uint32 chunk_size):
     - There are issues in selecting the leftmost argument
     - An offset is necessary to ensure alignment of chunks with forward
       pass
-    
+
     Hence, a separate 'reverse' variant of the function was implemented.
     """
     cdef uint32 seq_i
@@ -938,7 +936,7 @@ cdef _chunk_wise_reverse_argcummin(int64[:] values, uint32 chunk_size):
     cdef uint32 current_min_i = 0
     cdef int64 current_min, current_val
     cdef uint32[:] min_pos = np.empty(values.shape[0], dtype=np.uint32)
-    
+
     current_min = MAX_INT_64
     for seq_i in reversed(range(values.shape[0])):
         # The chunk beginning is a small difference to forward
@@ -952,5 +950,5 @@ cdef _chunk_wise_reverse_argcummin(int64[:] values, uint32 chunk_size):
             current_min_i = seq_i
             current_min = current_val
         min_pos[seq_i] = current_min_i
-    
+
     return min_pos

biotite/sequence/align/statistics.py

@@ -7,8 +7,8 @@ __author__ = "Patrick Kunzmann"
 __all__ = ["EValueEstimator"]
 
 import numpy as np
-from ..seqtypes import GeneralSequence
-from .pairwise import align_optimal
+from biotite.sequence.align.pairwise import align_optimal
+from biotite.sequence.seqtypes import GeneralSequence
 
 
 class EValueEstimator:
@@ -29,7 +29,7 @@ class EValueEstimator:
     of random sequence alignments in :meth:`from_samples()`
     :footcite:`Altschul1986`, which may be time consuming.
     If these parameters are known, the constructor can be used instead.
-    
+
     Based on the sampled parameters, the decadic logarithm of the
     E-value can be quickly calculated via :meth:`log_evalue()`.
 
@@ -39,7 +39,7 @@ class EValueEstimator:
         The :math:`\lambda` parameter.
     k : float
         The :math:`K` parameter.
-    
+
     Notes
     -----
     The calculated E-value is a rough estimation that gets more
@@ -102,8 +102,9 @@ class EValueEstimator:
         self._k = k
 
     @staticmethod
-    def from_samples(alphabet, matrix, gap_penalty, frequencies,
-                     sample_length=1000, sample_size=1000):
+    def from_samples(
+        alphabet, matrix, gap_penalty, frequencies, sample_length=1000, sample_size=1000
+    ):
         r"""
         Create an :class:`EValueEstimator` with :math:`\lambda` and
         :math:`K` estimated via sampling alignments of random sequences
@@ -137,13 +138,13 @@ class EValueEstimator:
             The number of sampled sequences.
             The accuracy of the estimated parameters and E-values,
             but also the runtime increases with the sample size.
-        
+
         Returns
         -------
         estimator : EValueEstimator
             A :class:`EValueEstimator` with sampled :math:`\lambda` and
             :math:`K` parameters.
-        
+
         Notes
         -----
         The sampling process generates random sequences based on
@@ -167,15 +168,15 @@ class EValueEstimator:
             raise ValueError("A symmetric substitution matrix is required")
         if not matrix.get_alphabet1().extends(alphabet):
             raise ValueError(
-                "The substitution matrix is not compatible "
-                "with the given alphabet"
+                "The substitution matrix is not compatible " "with the given alphabet"
             )
-        score_matrix = matrix.score_matrix()[:len(alphabet), :len(alphabet)]
-        if np.sum(
-            score_matrix \
-            * frequencies[np.newaxis, :] \
-            * frequencies[:, np.newaxis]
-        ) >= 0:
+        score_matrix = matrix.score_matrix()[: len(alphabet), : len(alphabet)]
+        if (
+            np.sum(
+                score_matrix * frequencies[np.newaxis, :] * frequencies[:, np.newaxis]
+            )
+            >= 0
+        ):
             raise ValueError(
                 "Invalid substitution matrix, the expected similarity "
                 "score between two random symbols is not negative"
@@ -183,9 +184,7 @@ class EValueEstimator:
 
         # Generate the sequence code for the random sequences
         random_sequence_code = np.random.choice(
-            len(alphabet),
-            size=(sample_size, 2, sample_length),
-            p=frequencies
+            len(alphabet), size=(sample_size, 2, sample_length), p=frequencies
         )
 
         # Sample the alignments of random sequences
@@ -193,28 +192,27 @@ class EValueEstimator:
         for i in range(sample_size):
             seq1 = GeneralSequence(alphabet)
             seq2 = GeneralSequence(alphabet)
-            seq1.code = random_sequence_code[i,0]
-            seq2.code = random_sequence_code[i,1]
+            seq1.code = random_sequence_code[i, 0]
+            seq2.code = random_sequence_code[i, 1]
             sample_scores[i] = align_optimal(
-                seq1, seq2, matrix,
-                local=True, gap_penalty=gap_penalty, max_number=1
+                seq1, seq2, matrix, local=True, gap_penalty=gap_penalty, max_number=1
             )[0].score
-        
+
         # Use method of moments to estimate parameters
         lam = np.pi / np.sqrt(6 * np.var(sample_scores))
         u = np.mean(sample_scores) - np.euler_gamma / lam
         k = np.exp(lam * u) / sample_length**2
-        
+
         return EValueEstimator(lam, k)
 
     @property
     def lam(self):
         return self._lam
-    
+
     @property
     def k(self):
         return self._k
-    
+
     def log_evalue(self, score, seq1_length, seq2_length):
         r"""
         Calculate the decadic logarithm of the E-value for a given
@@ -223,11 +221,11 @@ class EValueEstimator:
         The E-value and the logarithm of the E-value is calculated as
 
         .. math::
-        
+
             E = Kmn e^{-\lambda s}
 
             \log_{10} E = (\log_{10} Kmn) - \frac{\lambda s}{\ln 10},
-        
+
         where :math:`s` is the similarity score and :math:`m` and
         :math:`n` are the lengths of the aligned sequences.
 
@@ -245,12 +243,12 @@ class EValueEstimator:
             this is usually either the combined length of all sequences
             in the database or the length of the hit sequence multiplied
             by the number of sequences in the database.
-        
+
         Returns
         -------
         log_e : float
             The decadic logarithm of the E-value.
-        
+
         Notes
         -----
         This method returns the logarithm of the E-value instead of
@@ -261,5 +259,6 @@ class EValueEstimator:
         seq1_length = np.asarray(seq1_length)
         seq2_length = np.asarray(seq2_length)
 
-        return np.log10(self._k * seq1_length * seq2_length) \
-            - self._lam * score / np.log(10)
+        return np.log10(
+            self._k * seq1_length * seq2_length
+        ) - self._lam * score / np.log(10)