biotite 1.1.0__cp313-cp313-macosx_11_0_arm64.whl → 1.3.0__cp313-cp313-macosx_11_0_arm64.whl

biotite/sequence/align/alignment.py

@@ -19,6 +19,7 @@ __all__ = [
     "score",
     "find_terminal_gaps",
     "remove_terminal_gaps",
+    "remove_gaps",
 ]
 
 
@@ -303,7 +304,7 @@ def get_symbols(alignment):
 
     See Also
     --------
-    get_codes
+    get_codes : Get the sequence codes of the sequences in the alignment.
 
     Examples
     --------
@@ -361,9 +362,9 @@ def get_sequence_identity(alignment, mode="not_terminal"):
     identity : float
         The sequence identity, ranging between 0 and 1.
 
-    See also
+    See Also
     --------
-    get_pairwise_sequence_identity
+    get_pairwise_sequence_identity : Get sequence identity for each pair of alignment rows.
     """
     codes = get_codes(alignment)
 
@@ -424,9 +425,9 @@ def get_pairwise_sequence_identity(alignment, mode="not_terminal"):
     identity : ndarray, dtype=float, shape=(n,n)
         The pairwise sequence identity, ranging between 0 and 1.
 
-    See also
+    See Also
     --------
-    get_sequence_identity
+    get_sequence_identity : Get sequence identity over all alignment rows.
     """
     codes = get_codes(alignment)
     n_seq = len(codes)
@@ -489,10 +490,9 @@ def score(alignment, matrix, gap_penalty=-10, terminal_penalty=True):
         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. (Default: *-10*)
+        The values need to be negative.
     terminal_penalty : bool, optional
         If true, gap penalties are applied to terminal gaps.
-        (Default: True)
 
     Returns
     -------
@@ -569,9 +569,9 @@ def find_terminal_gaps(alignment):
         When these indices are used as slice index for an alignment or
         trace, the index would remove terminal gaps.
 
-    See also
+    See Also
     --------
-    remove_terminal_gaps
+    remove_terminal_gaps : Remove terminal gap columns directly.
 
     Examples
     --------
@@ -627,9 +627,9 @@ def remove_terminal_gaps(alignment):
         A shallow copy of the input `alignment` with an truncated trace,
         that does not contain alignment columns with terminal gaps.
 
-    See also
+    See Also
     --------
-    find_terminal_gaps
+    find_terminal_gaps : Only find terminal gap columns.
 
     Examples
     --------
@@ -666,6 +666,28 @@ def remove_terminal_gaps(alignment):
     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()`:

biotite/sequence/align/banded.pyx

@@ -54,7 +54,7 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
     aligned to each other, if :math:`D_L \leq j - i \leq D_U`.
     With increasing width of the diagonal band, the probability to find
     the optimal alignment, but also the computation time increases.
-    
+
     Parameters
     ----------
     seq1, seq2 : Sequence
@@ -76,7 +76,7 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
         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. (Default: *-10*)
+        The values need to be negative.
     local : bool, optional
         If set to true, a local alignment is performed.
         Otherwise (default) a semi-global alignment is performed.
@@ -84,15 +84,15 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
         The maximum number of alignments returned.
         When the number of branches exceeds this value in the traceback
         step, no further branches are created.
-    
+
     Returns
     -------
     alignments : list of Alignment
         The generated alignments.
         Each alignment in the list has the same similarity score,
         which is the maximum score possible within the defined band.
-    
-    See also
+
+    See Also
     --------
     align_optimal
         Guarantees to find the optimal alignment at the cost of greater
@@ -110,7 +110,7 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
     yield a more optimal alignment.
     Considerations on how to find a suitable band width are discussed in
     :footcite:`Gibrat2018`.
-    
+
     The restriction to a limited band is the central difference between
     the banded alignment heuristic and the optimal alignment
     algorithms :footcite:`Needleman1970, Smith1981`.
@@ -151,12 +151,12 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
     Filled cells, i.e. cells within the band, are indicated by ``x``.
     The shorter sequence is always represented by the first dimension
     of the table in this implementation.
-    
+
     References
     ----------
-    
+
     .. footbibliography::
-    
+
     Examples
     --------
 
@@ -203,7 +203,7 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
         raise ValueError(
             "Maximum number of returned alignments must be at least 1"
         )
-    
+
     # The shorter sequence is the one on the left of the matrix
     # -> shorter sequence is 'seq1'
     if len(seq2) < len(seq1):
@@ -243,11 +243,11 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
     trace_table = np.zeros((len(seq1)+1, band_width+2), dtype=np.uint8)
     code1 = seq1.code
     code2 = seq2.code
-    
+
 
     # Table filling
     ###############
-    
+
     # A score value that signals that the respective direction in the
     # dynamic programming matrix should not be used, since it would be
     # outside the band
@@ -294,7 +294,7 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
             code1, code2, matrix.score_matrix(), trace_table, score_table,
             lower_diag, upper_diag, gap_penalty, local
         )
-    
+
 
     # Traceback
     ###########
@@ -383,7 +383,7 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
             state_list = np.full(
                 len(i_list), TraceState.NO_STATE, dtype=int
             )
-    
+
     # Follow the traces specified in state and indices lists
     cdef int curr_trace_count
     for k in range(len(i_list)):
@@ -401,7 +401,7 @@ def align_banded(seq1, seq2, matrix, band, gap_penalty=-10, local=False,
             curr_trace_count=&curr_trace_count, max_trace_count=max_number,
             lower_diag=lower_diag, upper_diag=upper_diag
         )
-    
+
     # Replace gap entries in trace with -1
     for i, trace in enumerate(trace_list):
         trace = np.flip(trace, axis=0)
@@ -459,7 +459,7 @@ def _fill_align_table(CodeType1[:] code1 not None,
     local
         Indicates, whether a local alignment should be performed.
     """
-    
+
     cdef int i, j
     cdef int seq_i, seq_j
     cdef int32 from_diag, from_left, from_top
@@ -488,7 +488,7 @@ def _fill_align_table(CodeType1[:] code1 not None,
             from_top  = score_table[i-1, j+1] + gap_penalty
 
             trace = get_trace_linear(from_diag, from_left, from_top, &score)
-            
+
             # Local alignment specialty:
             # If score is less than or equal to 0,
             # then 0 is saved on the field and the trace ends here
@@ -541,7 +541,7 @@ def _fill_align_table_affine(CodeType1[:] code1 not None,
     local
         Indicates, whether a local alignment should be performed.
     """
-    
+
     cdef int i, j
     cdef int seq_i, seq_j
     cdef int32 mm_score, g1m_score, g2m_score
@@ -550,7 +550,7 @@ def _fill_align_table_affine(CodeType1[:] code1 not None,
     cdef uint8 trace
     cdef int32 m_score, g1_score, g2_score
     cdef int32 similarity_score
-    
+
     # Starts at 1 since the first row and column are already fil
     for seq_i in range(0, code1.shape[0]):
         i = seq_i + 1
@@ -572,7 +572,7 @@ def _fill_align_table_affine(CodeType1[:] code1 not None,
             g1g1_score = g1_table[i, j-1] + gap_ext
             mg2_score  =  m_table[i-1, j+1] + gap_open
             g2g2_score = g2_table[i-1, j+1] + gap_ext
-            
+
             trace = get_trace_affine(
                 mm_score, g1m_score, g2m_score,
                 mg1_score, g1g1_score,
@@ -600,7 +600,7 @@ def _fill_align_table_affine(CodeType1[:] code1 not None,
                     m_table[i,j] = m_score
                 if g1_score <= 0:
                     trace &= ~(
-                        TraceDirectionAffine.MATCH_TO_GAP_LEFT | 
+                        TraceDirectionAffine.MATCH_TO_GAP_LEFT |
                         TraceDirectionAffine.GAP_LEFT_TO_GAP_LEFT
                     )
                     # g1_table[i,j] remains negative infinity
@@ -623,7 +623,7 @@ def _fill_align_table_affine(CodeType1[:] code1 not None,
 
 def get_global_trace_starts(seq1_len, seq2_len, lower_diag, upper_diag):
     band_width = upper_diag - lower_diag + 1
-    
+
     j = np.arange(1, band_width + 1)
     seq_j = j + (seq1_len-1) + lower_diag - 1
     # Start from the end from the first (shorter) sequence,

biotite/sequence/align/cigar.py

@@ -86,7 +86,7 @@ def read_alignment_from_cigar(cigar, position, reference_sequence, segment_seque
 
     See Also
     --------
-    write_alignment_to_cigar
+    write_alignment_to_cigar : The reverse operation.
 
     Notes
     -----
@@ -253,7 +253,7 @@ def write_alignment_to_cigar(
 
     See Also
     --------
-    read_alignment_from_cigar
+    read_alignment_from_cigar : The reverse operation.
 
     Notes
     -----

biotite/sequence/align/kmeralphabet.pyx

@@ -267,7 +267,7 @@ class KmerAlphabet(Alphabet):
         kmer_codes : int or ndarray, dtype=np.int64, shape=(n,)
             The fused *k-mer* code(s).
 
-        See also
+        See Also
         --------
         split
             The reverse operation.
@@ -319,7 +319,7 @@ class KmerAlphabet(Alphabet):
         codes : ndarray, dtype=np.uint64, shape=(k,) or shape=(n,k)
             The split symbol codes from the base alphabet.
 
-        See also
+        See Also
         --------
         fuse
             The reverse operation.

biotite/sequence/align/kmertable.pyx

@@ -102,7 +102,7 @@ cdef class KmerTable:
     k : int
         The length of the *k-mers*.
 
-    See also
+    See Also
     --------
     BucketKmerTable
 
@@ -308,7 +308,7 @@ cdef class KmerTable:
             The number of *informative* positions must equal *k*.
             Refer to :class:`KmerAlphabet` for more details.
 
-        See also
+        See Also
         --------
         from_kmers : The same functionality based on already created *k-mers*
 
@@ -413,7 +413,7 @@ cdef class KmerTable:
             is false, is not added to the table.
             By default, all positions are added.
 
-        See also
+        See Also
         --------
         from_sequences : The same functionality based on undecomposed sequences
 
@@ -1548,7 +1548,7 @@ cdef class BucketKmerTable:
     n_buckets : int
         The number of buckets, the *k-mers* are divided into.
 
-    See also
+    See Also
     --------
     KmerTable
 
@@ -1774,7 +1774,7 @@ cdef class BucketKmerTable:
             purpose.
             By default, a load factor of approximately 0.8 is used.
 
-        See also
+        See Also
         --------
         from_kmers : The same functionality based on already created *k-mers*
 
@@ -1892,7 +1892,7 @@ cdef class BucketKmerTable:
             purpose.
             By default, a load factor of approximately 0.8 is used.
 
-        See also
+        See Also
         --------
         from_sequences : The same functionality based on undecomposed sequences