sequence alignment operators

Genentech · Apr 22, 2024 · 40181a9 · 40181a9
1 parent c7d2b4c
commit 40181a9
Show file tree

Hide file tree

Showing 6 changed files with 5,246 additions and 4 deletions.
diff --git a/.gitignore b/.gitignore
@@ -11,4 +11,5 @@
 .ruff_cache/
 __pycache__/
 build/
-dist/
+dist/
+notebooks/
diff --git a/notebooks/scoring_matricies.ipynb b/notebooks/scoring_matricies.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -28,6 +28,7 @@ exclude = [
     "./src/beignet/constants/_blosum80.py",
     "./src/beignet/constants/_blosum90.py",
     "./src/beignet/constants/_blosum_vocabulary.py",
+    "./src/beignet/constants/_substitution_matrix.py",
 ]
 
 [tool.ruff.lint]

diff --git a/src/beignet/constants/__init__.py b/src/beignet/constants/__init__.py
@@ -4,6 +4,58 @@
 from ._blosum80 import BLOSUM80
 from ._blosum90 import BLOSUM90
 from ._blosum_vocabulary import BLOSUM_VOCABULARY
+from ._substitution_matrix import (
+    PAM10,
+    PAM20,
+    PAM30,
+    PAM40,
+    PAM50,
+    PAM60,
+    PAM70,
+    PAM80,
+    PAM90,
+    PAM100,
+    PAM110,
+    PAM120,
+    PAM130,
+    PAM140,
+    PAM150,
+    PAM160,
+    PAM170,
+    PAM180,
+    PAM190,
+    PAM200,
+    PAM210,
+    PAM220,
+    PAM230,
+    PAM240,
+    PAM250,
+    PAM260,
+    PAM270,
+    PAM280,
+    PAM290,
+    PAM300,
+    PAM310,
+    PAM320,
+    PAM330,
+    PAM340,
+    PAM350,
+    PAM360,
+    PAM370,
+    PAM380,
+    PAM390,
+    PAM400,
+    PAM410,
+    PAM420,
+    PAM430,
+    PAM440,
+    PAM450,
+    PAM460,
+    PAM470,
+    PAM480,
+    PAM490,
+    PAM500,
+)
 
 __all__ = [
     "BLOSUM45",
@@ -12,4 +64,54 @@
     "BLOSUM80",
     "BLOSUM90",
     "BLOSUM_VOCABULARY",
+    "PAM10",
+    "PAM20",
+    "PAM30",
+    "PAM40",
+    "PAM50",
+    "PAM60",
+    "PAM70",
+    "PAM80",
+    "PAM90",
+    "PAM100",
+    "PAM110",
+    "PAM120",
+    "PAM130",
+    "PAM140",
+    "PAM150",
+    "PAM160",
+    "PAM170",
+    "PAM180",
+    "PAM190",
+    "PAM200",
+    "PAM210",
+    "PAM220",
+    "PAM230",
+    "PAM240",
+    "PAM250",
+    "PAM260",
+    "PAM270",
+    "PAM280",
+    "PAM290",
+    "PAM300",
+    "PAM310",
+    "PAM320",
+    "PAM330",
+    "PAM340",
+    "PAM350",
+    "PAM360",
+    "PAM370",
+    "PAM380",
+    "PAM390",
+    "PAM400",
+    "PAM410",
+    "PAM420",
+    "PAM430",
+    "PAM440",
+    "PAM450",
+    "PAM460",
+    "PAM470",
+    "PAM480",
+    "PAM490",
+    "PAM500",
 ]