Manacher

pyproject.toml

@@ -14,7 +14,7 @@ classifiers = [
   "Programming Language :: Python :: 3",
   "Intended Audience :: Science/Research",
   "Topic :: Scientific/Engineering",
-  "Topic :: Scientific/Engineering :: Bio-Informatics"
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dynamic = ["version", "readme", "dependencies"]
 
@@ -28,7 +28,7 @@ readme = { file = ["README.md"], content-type = "text/markdown" }
 dependencies = { file = ["requirements.txt"] }
 
 [tool.setuptools]
-package-dir = { "" = "src"}
+package-dir = { "" = "src" }
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -95,7 +95,14 @@ max-line-length = 88
 
 [tool.pylint."messages control"]
 disable = [
-  "R1731" # consider-using-max-builtin
+  "R1731", # consider-using-max-builtin
+  "E0401", # import-error
+]
+
+[tool.pylint."*.pyi"]
+disable = [
+  "W0613", # unused-argument
+  "W0231", # super-init-not-called
 ]
 
 [tool.ruff]

setup.py

@@ -66,6 +66,14 @@
         # extra_link_args=[openmp],
     )
 )
+extensions.append(
+    Extension(
+        "designer_dna._oligonucleotides",
+        ["src/designer_dna/_oligonucleotides.pyx"],
+        include_dirs=["src/designer_dna/headers"],
+        language="c++",
+    )
+)
 
 
 # Add cython directive to specify python version target

src/designer_dna/_oligonucleotides.pyi

@@ -0,0 +1,48 @@
+# BSD 3-Clause License
+#
+# Copyright (c) 2025, Spill-Tea
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its
+#    contributors may be used to endorse or promote products derived from
+#    this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+"""Oligonucleotide functions with the help of C++."""
+
+def manacher(sequence: str, dna: bool = ...) -> str:
+    """Find the longest palindromic substring within a nucleotide sequence.
+
+    Args:
+        sequence (str): Nucleotide sequence string.
+        dna (bool): Sequence is DNA, else RNA.
+
+    Returns:
+        (str): longest palindromic substring within sequence.
+
+    Notes:
+        * This is a cython/c++ implementation of the O(n) Manacher's algorithm.
+        * This algorithm is typically slower than the O(nlogn) palindrome function for
+          strings up to 2^23 characters (not benchmarked beyond this limit).
+        * This function here is primarily here for demonstration purposes.
+
+    """

src/designer_dna/_oligonucleotides.pyx

@@ -0,0 +1,127 @@
+# BSD 3-Clause License
+#
+# Copyright (c) 2025, Spill-Tea
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its
+#    contributors may be used to endorse or promote products derived from
+#    this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+# distutils: language = c++
+
+"""Oligonucleotide functions with the help of C++."""
+from narray cimport NumericArray
+from designer_dna._oligos cimport v_complement
+from common cimport StringView, str_to_view
+from libc.stdlib cimport free
+
+
+cdef extern from "Python.h":
+    str PyUnicode_Join(str, str)
+
+
+cdef inline void _compute(
+    char* s,
+    char* c,
+    NumericArray[int]* arr,
+    ssize_t n,
+):
+    cdef:
+        ssize_t mirror, a, b, i, stemp, center = 0, radius = 0
+        int temp, zero = 0
+
+    for i in range(1, n - 1):
+        # parity: 0 1 0 1 0 1 0 1 0
+        # string: ^ # A # N # T # $
+        #  index: 0 1 2 3 4 5 6 7 8
+
+        # skip odd length palindromes (when index is centered on an even position)
+        # if character from ref seq and complement do not match
+        if i % 2 == 0 and s[i] != c[i]:
+            arr[0][i] = zero
+            continue
+
+        # Look ahead at mirror position
+        mirror = 2 * center - i
+        if i < radius:
+            temp = <int> (radius - i)
+            arr[0][i] = min(temp, arr[0][mirror])
+        else:
+            arr[0][i] = zero
+
+        # Center expansion method
+        stemp = <ssize_t> arr[0][i]
+        a = i + 1 + stemp
+        b = i - 1 - stemp
+        while s[a] == c[b] and s[b] == c[a]:
+            arr[0][i] += 1
+            a += 1
+            b -= 1
+
+        stemp = <ssize_t> arr[0][i]
+        if i + stemp > radius:
+            center = i
+            radius = i + stemp
+
+
+cpdef str manacher(str sequence, bint dna = True):
+    """Find the longest palindromic substring within a nucleotide sequence.
+
+    Args:
+        sequence (str): Nucleotide sequence string.
+        dna (bool): Sequence is DNA, else RNA.
+
+    Returns:
+        (str): longest palindromic substring within sequence.
+
+    Notes:
+        * This is a cython/c++ implementation of the O(n) Manacher's algorithm.
+        * This algorithm is typically slower than the O(nlogn) palindrome function for
+          strings up to 2^23 characters (not benchmarked beyond this limit).
+        * This function here is primarily here for demonstration purposes.
+
+    """
+    cdef:
+        str k = PyUnicode_Join("#", f"^{sequence}$")
+        StringView ref = str_to_view(k)
+        StringView com = str_to_view(k)
+        NumericArray[int]* arr
+        ssize_t i, center = 0
+        int radius = 0
+
+    arr = new NumericArray[int](ref.size)
+    arr.fill(radius)
+    v_complement(&com, dna)
+
+    _compute(ref.ptr, com.ptr, arr, <ssize_t> ref.size)
+    free(ref.ptr)
+    free(com.ptr)
+
+    # Enumerate, capturing index (center) and value of max (radius)
+    for i in range(1, ref.size - 1):
+        if arr[0][i] > radius:
+            radius = arr[0][i]
+            center = i
+    del arr
+
+    return k[center - radius + 1: center + radius: 2]

src/designer_dna/_oligos.pxd

@@ -0,0 +1,40 @@
+# BSD 3-Clause License
+#
+# Copyright (c) 2025, Spill-Tea
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its
+#    contributors may be used to endorse or promote products derived from
+#    this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+from common cimport StringView
+
+cdef:
+    void c_reverse(char*, Py_ssize_t)
+    void v_reverse(StringView*)
+
+    void c_complement(char*, Py_ssize_t, unsigned char*)
+    void v_complement(StringView*, bint)
+
+    void c_reverse_complement(char*, Py_ssize_t, unsigned char*)
+    void v_reverse_complement(StringView*, bint)

src/designer_dna/_oligos.pyi

@@ -27,8 +27,6 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-# pylint: disable=W0613
-
 """Cythonized oligonucleotide functions."""
 
 def reverse(sequence: str) -> str:
@@ -70,7 +68,7 @@ def reverse_complement(sequence: str, dna: bool = ...) -> str:
     """Reverse complement a nucleotide sequence.
 
     Args:
-        sequence (str): Nucelotide sequence string.
+        sequence (str): Nucleotide sequence string.
         dna (bool): Sequence is DNA, else RNA.
 
     Returns: