Merge pull request #13 from not-a-feature/dev

Update to v2.0.1: two-key structure

.github/workflows/tests.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ['3.7', '3.10', '3.11']
 
     steps:

DEPENDENCIES.md

@@ -7,7 +7,7 @@ Any information relevant to third-party vendors listed below are collected using
 
 ## Dependencies
 
-### [mypy (0.930)](http://www.mypy-lang.org/)
+### [mypy](http://www.mypy-lang.org/)
 
 #### Declared Licenses
 MIT *OR* Python-2.0
@@ -17,7 +17,7 @@ MIT *OR* Python-2.0
 **Package Homepage**: http://www.mypy-lang.org/
 ---
 
-### [pytest (7.0.0rc1)](http://pytest.org)
+### [pytest](http://pytest.org)
 
 #### Declared Licenses
 
@@ -27,7 +27,7 @@ MIT *OR* Python-2.0
 
 ---
 
-### [pytest-cov (3.0.0)](https://github.com/pytest-dev/pytest-cov)
+### [pytest-cov](https://github.com/pytest-dev/pytest-cov)
 
 #### Declared Licenses
 MIT
@@ -38,7 +38,7 @@ MIT
 
 ---
 
-### [tox (4.0.0a9)](https://tox.readthedocs.org/)
+### [tox](https://tox.readthedocs.org/)
 
 #### Declared Licenses
 MIT

README.md

@@ -14,7 +14,7 @@ The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between p
 Reading such matrices is not particularly difficult, yet most off the shelf packages are overloaded with strange dependencies.
 And why do we need to implement the same reader again if there is a simple module for that.
 
-`blosum` offers a robust and easy-to-expand implementation without relying on third-party libraries. 
+`blosum` offers a robust and easy-to-expand implementation without relying on third-party libraries.
 
 
 ## Installation
@@ -35,22 +35,24 @@ conda install blosum
 ```
 ## How to use
 
-### Default BLOSUM 
+### Default BLOSUM
 This package provides the most commonly used BLOSUM matrices.
 You can choose from BLOSUM 45, 50, 62, 80 and 90.
 
 To load a matrix:
 ```python
 import blosum as bl
 matrix = bl.BLOSUM(62)
-``` 
+val = matrix["A"]["Y"]
+```
 
 ### Custom matrix
 In addition, own matrices can be loaded. For this, the path is given as an argument.
 
 ```python
 import blosum as bl
 matrix = bl.BLOSUM("path/to/blosum.file")
+val = matrix["A"]["Y"]
 ```
 
 The matrices are required to have following format:
@@ -70,18 +72,24 @@ Once loaded the `matrix` behaves like a `defaultdict`.
 To get a value use:
 
 ```python
-val = matrix["AY"]
+val = matrix["A"]["Y"]
 ```
+To get a defaultdict of the row with a given key use:
+
+```python
+val_dict = matrix["A"]
+```
+
 
-If the key cannot be found, the default value is returned. It is `float("-inf")`.
+If the key cannot be found, the default value `float("-inf")` is returned.
 It is possible to set a custom default score:
 ```python
 matrix = bl.BLOSUM(62, default=0)
 ```
 
 ## License
 ```
-Copyright (C) 2022 by Jules Kreuer - @not_a_feature
+Copyright (C) 2023 by Jules Kreuer - @not_a_feature
 This piece of software is published unter the GNU General Public License v3.0
 TLDR:
 

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = blosum
-version = 1.2.2
+version = 2.0.1
 description = A simple BLOSUM toolbox without dependencies.
 long_description = file: README.md
 long_description_content_type=text/markdown

src/blosum/_blosum.py

@@ -14,33 +14,39 @@
 
 
 class BLOSUM(defaultdict):  # type: ignore
-    def __init__(self, n, default: float = float("-inf")):
+    def __init__(self, n: Union[int, str], default: float = float("-inf")):
         """
         Object to easily access a blosum matrix.
         This reader supports asymetric data.
 
-        Input:
-        Either n ϵ {45,50,62,80,90} or path
+        Input
+        -----
+            Either n ϵ {45,50,62,80,90} or path
 
-        n: Int, which BLOSUM Matrix to use.
-            Choice between: 45,50,62,80 and 90
-            Data gathered from https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/
+            n: int, which BLOSUM Matrix to use.
+                Choice between: 45,50,62,80 and 90
+                Data gathered from https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/
 
-        path: String, path to a Blosum matrix.
-            File in a format like:
-            https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM62
+            path: string, path to a Blosum matrix.
+                File in a format like:
+                https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM62
+
+            default: float, default -inf
         """
 
         self.n = n
         self.default = default
 
         # Using default matrix
-        if n in [45, 50, 62, 80, 90]:
-            super().__init__(lambda: default, default_blosum[n])
+        if isinstance(n, int) and n in [45, 50, 62, 80, 90]:
+            matrix = {}
+            for k, v in default_blosum[n].items():
+                matrix[k] = defaultdict(lambda: default, v)
+            super().__init__(lambda: defaultdict(lambda: default), matrix)
 
         # load custom matrix
         elif isinstance(n, str):
-            super().__init__(lambda: default, loadMatrix(n))
+            super().__init__(lambda: defaultdict(lambda: default), loadMatrix(n))
         else:
             raise (
                 BaseException(
@@ -73,23 +79,31 @@ def __repr__(self) -> str:
         return f"BLOSUM({n}, default={d})"
 
 
-def loadMatrix(path: str) -> Union[Dict[str, int], Dict[str, float]]:
+def loadMatrix(
+    path: str,
+    default: float = float("-inf"),
+) -> DefaultDict[str, DefaultDict[str, float]]:
     """
     Reads a Blosum matrix from file.
     File in a format like:
         https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM62
 
-    Input:
+    Input
+    -----
         path: str, path to a file.
+        default: float, default value "-inf"
 
-    Returns:
+    Returns
+    -------
         blosumDict: Dictionary, The blosum dict
     """
 
     with open(path, "r") as f:
         content = f.readlines()
 
-    blosumDict = {}
+    blosumDict: DefaultDict[str, DefaultDict[str, float]] = defaultdict(
+        lambda: defaultdict(lambda: default)
+    )
 
     header = True
     for line in content:
@@ -117,9 +131,10 @@ def loadMatrix(path: str) -> Union[Dict[str, int], Dict[str, float]]:
 
         # Add Line/Label combination to dict
         for index, lab in enumerate(labelslist, start=1):
-            blosumDict[f"{linelist[0]}{lab}"] = float(linelist[index])
+            blosumDict[linelist[0]][lab] = float(linelist[index])
 
     # Check quadratic
-    if not len(blosumDict) == len(labelslist) ** 2:
+    if not len(blosumDict) == len(labelslist):
         raise EOFError("Blosum file is not quadratic.")
+
     return blosumDict