biotite 0.41.2__cp312-cp312-macosx_11_0_arm64.whl → 1.0.0__cp312-cp312-macosx_11_0_arm64.whl

biotite/sequence/align/alignment.py

@@ -5,16 +5,22 @@
 __name__ = "biotite.sequence.align"
 __author__ = "Patrick Kunzmann"
 
-import numpy as np
 import numbers
-import copy
 import textwrap
-from ..alphabet import LetterAlphabet
-
+from collections.abc import Sequence
+import numpy as np
+from biotite.sequence.alphabet import LetterAlphabet
 
-__all__ = ["Alignment", "get_codes", "get_symbols",
-           "get_sequence_identity", "get_pairwise_sequence_identity",
-           "score", "find_terminal_gaps", "remove_terminal_gaps"]
+__all__ = [
+    "Alignment",
+    "get_codes",
+    "get_symbols",
+    "get_sequence_identity",
+    "get_pairwise_sequence_identity",
+    "score",
+    "find_terminal_gaps",
+    "remove_terminal_gaps",
+]
 
 
 class Alignment(object):
@@ -22,7 +28,7 @@ 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.
@@ -31,16 +37,16 @@ class Alignment(object):
     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
@@ -49,7 +55,7 @@ class Alignment(object):
         The alignment trace.
     score : int, optional
         Alignment score.
-    
+
     Attributes
     ----------
     sequences : list
@@ -58,10 +64,10 @@ class Alignment(object):
         The alignment trace.
     score : int
         Alignment score.
-    
+
     Examples
     --------
-    
+
     >>> seq1 = NucleotideSequence("CGTCAT")
     >>> seq2 = NucleotideSequence("TCATGC")
     >>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
@@ -95,8 +101,10 @@ class Alignment(object):
 
     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})"
+        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 = ""
@@ -107,11 +115,11 @@ class Alignment(object):
             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
@@ -119,7 +127,7 @@ class Alignment(object):
             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
@@ -143,32 +151,33 @@ class Alignment(object):
             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"
-                    )
+            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
+                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
@@ -179,45 +188,41 @@ class Alignment(object):
         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]
+        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__}'"
-            )
-    
+            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"
-            )
+            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)
+        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])):
@@ -238,22 +243,22 @@ def get_codes(alignment):
     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()
@@ -267,14 +272,17 @@ def get_codes(alignment):
     """
     trace = alignment.trace
     sequences = alignment.sequences
-    
+
     # The number of sequences is the first dimension
-    codes = np.zeros((trace.shape[1], trace.shape[0]), dtype=int)
+    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]], -1
+            trace[:, i] != -1, sequences[i].code[trace[:, i]], np.int64(-1)
         )
-    
+
     return np.stack(codes)
 
 
@@ -283,24 +291,24 @@ 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
 
     Examples
     --------
-    
+
     >>> seq1 = NucleotideSequence("CGTCAT")
     >>> seq2 = NucleotideSequence("TCATGC")
     >>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
@@ -317,8 +325,8 @@ def get_symbols(alignment):
         alphabet = alignment.sequences[i].get_alphabet()
         codes_wo_gaps = codes[i, codes[i] != -1]
         symbols_wo_gaps = alphabet.decode_multiple(codes_wo_gaps)
-        if not isinstance(symbols_wo_gaps, list):
-            symbols_wo_gaps = list(symbols_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()
@@ -331,7 +339,7 @@ def get_sequence_identity(alignment, mode="not_terminal"):
 
     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
@@ -348,12 +356,12 @@ def get_sequence_identity(alignment, mode="not_terminal"):
               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
@@ -363,12 +371,12 @@ def get_sequence_identity(alignment, mode="not_terminal"):
     # Count matches
     matches = 0
     for i in range(codes.shape[1]):
-        column = codes[:,i]
+        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)
@@ -394,7 +402,7 @@ def get_pairwise_sequence_identity(alignment, mode="not_terminal"):
 
     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
@@ -411,12 +419,12 @@ def get_pairwise_sequence_identity(alignment, mode="not_terminal"):
               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
@@ -427,9 +435,11 @@ def get_pairwise_sequence_identity(alignment, mode="not_terminal"):
     # 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) \
+    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)
 
@@ -441,24 +451,23 @@ def get_pairwise_sequence_identity(alignment, mode="not_terminal"):
         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]])
+                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
+                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])
-                ])
+                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
 
 
@@ -468,7 +477,7 @@ def score(alignment, matrix, gap_penalty=-10, terminal_penalty=True):
 
     If the alignment contains more than two sequences,
     all pairwise scores are counted.
-    
+
     Parameters
     ----------
     alignment : Alignment
@@ -485,7 +494,7 @@ def score(alignment, matrix, gap_penalty=-10, terminal_penalty=True):
     terminal_penalty : bool, optional
         If true, gap penalties are applied to terminal gaps.
         (Default: True)
-    
+
     Returns
     -------
     score : int
@@ -503,18 +512,18 @@ def score(alignment, matrix, gap_penalty=-10, terminal_penalty=True):
         # 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]):
+            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 type(gap_penalty) == int:
+    if isinstance(gap_penalty, numbers.Real):
         gap_open = gap_penalty
         gap_ext = gap_penalty
-    elif type(gap_penalty) == tuple:
+    elif isinstance(gap_penalty, Sequence):
         gap_open = gap_penalty[0]
         gap_ext = gap_penalty[1]
     else:
@@ -590,15 +599,15 @@ def find_terminal_gaps(alignment):
     """
     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])]
+    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])]
+    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), np.min(lasts) + 1
+    return np.max(firsts).item(), np.min(lasts).item() + 1
 
 
 def remove_terminal_gaps(alignment):
@@ -655,4 +664,4 @@ def remove_terminal_gaps(alignment):
             "Cannot remove terminal gaps, since at least two sequences have "
             "no overlap and the resulting alignment would be empty"
         )
-    return alignment[start : stop]
+    return alignment[start:stop]

biotite/sequence/align/buckets.py

@@ -6,11 +6,12 @@ __name__ = "biotite.sequence.align"
 __author__ = "Patrick Kunzmann"
 __all__ = ["bucket_number"]
 
-from os.path import realpath, dirname, join
+from os.path import dirname, join, realpath
 import numpy as np
 
-
 _primes = None
+
+
 def bucket_number(n_kmers, load_factor=0.8):
     """
     Find an appropriate number of buckets for a :class:`BucketKmerTable`
@@ -54,16 +55,17 @@ def bucket_number(n_kmers, load_factor=0.8):
     """
     global _primes
     if _primes is None:
-        with open(
-            join(dirname(realpath(__file__)), "primes.txt")
-        ) as file:
-            _primes = np.array([
-                int(line) for line in file.read().splitlines()
-                if len(line) != 0 and line[0] != "#"
-            ])
+        with open(join(dirname(realpath(__file__)), "primes.txt")) as file:
+            _primes = np.array(
+                [
+                    int(line)
+                    for line in file.read().splitlines()
+                    if len(line) != 0 and line[0] != "#"
+                ]
+            )
 
     number = int(n_kmers / load_factor)
     index = np.searchsorted(_primes, number, side="left")
     if index == len(_primes):
         raise ValueError("Number of buckets too large")
-    return _primes[index]
+    return _primes[index]