blosum - npm Package Compare versions

Comparing version 1.2.2 to 2.0.1

tests/test_blosum.py

+# Testing BLOSUM Handling
+import blosum as bl
+import pytest
+from os import path
+
+
+f = float("-inf")
+
+
[e-mail](
+    "blosum_number,expected",
+    [
+        (45, [0, 1, -2, -5, 3, 1, -3, -5, -2, -2, 1, -5, f, f, f, f]),
+        (50, [0, 1, -1, -5, 3, 2, -4, -5, -3, -1, 1, -5, f, f, f, f]),
+        (62, [0, 0, -1, -4, 2, 1, -3, -4, -3, -2, 1, -4, f, f, f, f]),
+        (90, [0, 1, -2, -6, 2, 1, -4, -6, -4, -3, 0, -6, f, f, f, f]),
+    ],
+)
+def test_blosum(blosum_number, expected):
+    bm = bl.BLOSUM(blosum_number)
+
+    get_test = []
+
+    for a in ["H", "K", "W", "U"]:
+        for b in ["R", "Q", "F", "*"]:
+            get_test.append(bm[a][b])
+
+    assert get_test == expected
+
+
+def test_blosum_default():
+    bm = bl.BLOSUM(62, default=-99)
+    assert bm["non"]["existent"] == -99  # test default value
+    assert dict(bm["nonexistent"]) == dict()  # test default value
+    assert bm["H"]["F"] == -1  # test real value
+
+
[e-mail]("ignore:Blosum")
+def test_blosum_custom_file():
+    fp = path.join(path.dirname(__file__), "test.blosum")
+    bm = bl.BLOSUM(fp)
+    labels = ["A", "R", "N", "D"]
+    s = sum([bm[a][b] for b in labels for a in labels])
+    assert s == 19
+
+
[e-mail]("ignore:Blosum")
+def test_blosum_custom_file_with_comments():
+    fp = path.join(path.dirname(__file__), "comments.blosum")
+    bm = bl.BLOSUM(fp)
+    labels = ["A", "R", "N", "D"]
+    s = sum([bm[a][b] for b in labels for a in labels])
+    assert s == 17
+
+
[e-mail]
+def test_blosum_invalid_file():
+    fp = path.join(path.dirname(__file__), "fail.blosum")
+    bm = bl.BLOSUM(fp)
+    bm["A"]["B"]
+
+
[e-mail]
+def test_blosum_invalid_file2():
+    fp = path.join(path.dirname(__file__), "fail2.blosum")
+    bm = bl.BLOSUM(fp)
+    bm["A"]["B"]
+
+
[e-mail]
+def test_blosum_empty():
+    bm = bl.BLOSUM(None)
+    bm["A"]["B"]
+
+
+def test_magic_repr():
+    assert repr(bl.BLOSUM(62)) == "BLOSUM(62, default=float('-inf'))"
+    assert repr(bl.BLOSUM(62, default=float("inf"))) == "BLOSUM(62, default=float('inf'))"
+    assert repr(bl.BLOSUM(62, default=0)) == "BLOSUM(62, default=0)"
+
+    fp = path.join(path.dirname(__file__), "test.blosum")
+    assert repr(bl.BLOSUM(fp, default=0)) == f'BLOSUM("{fp}", default=0)'

tests/test_loadMatrix.py

+# Testing BLOSUM Handling
+import blosum as bl
+import pytest
+from os import path
+
+
+f = float("-inf")
+
+
[e-mail]("ignore:Blosum")
+def test_loadMatrix_eq_blosum():
+    fp = path.join(path.dirname(__file__), "test.blosum")
+    bm = dict(bl.BLOSUM(fp))
+
+    assert bm == bl.loadMatrix(fp)

PKG-INFO

 Metadata-Version: 2.1
 Name: blosum
-Version: 1.2.2
+Version: 2.0.1
 Summary: A simple BLOSUM toolbox without dependencies.
@@ -41,3 +41,3 @@ Home-page: https://github.com/not-a-feature/blosum
 
-`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.
 
@@ -63,3 +63,3 @@
 
-### Default BLOSUM 
+### Default BLOSUM
 This package provides the most commonly used BLOSUM matrices.
@@ -72,3 +72,4 @@ You can choose from BLOSUM 45, 50, 62, 80 and 90.
 matrix = bl.BLOSUM(62)
-``` 
+val = matrix["A"]["Y"]
+```
 
@@ -81,2 +82,3 @@ ### Custom matrix
 matrix = bl.BLOSUM("path/to/blosum.file")
+val = matrix["A"]["Y"]
 ```
@@ -101,6 +103,12 @@
 ```python
-val = matrix["AY"]
+val = matrix["A"]["Y"]
 ```
+To get a defaultdict of the row with a given key use:
 
-If the key cannot be found, the default value is returned. It is `float("-inf")`.
+```python
+val_dict = matrix["A"]
+```
+
+
+If the key cannot be found, the default value `float("-inf")` is returned.
 It is possible to set a custom default score:
@@ -113,3 +121,3 @@ ```python
 ```
-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
@@ -116,0 +124,0 @@ TLDR:

README.md

@@ -17,3 +17,3 @@ ![blosum](https://github.com/not-a-feature/blosum/raw/main/blosum.png)
 
-`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.
 
@@ -39,3 +39,3 @@
 
-### Default BLOSUM 
+### Default BLOSUM
 This package provides the most commonly used BLOSUM matrices.
@@ -48,3 +48,4 @@ You can choose from BLOSUM 45, 50, 62, 80 and 90.
 matrix = bl.BLOSUM(62)
-``` 
+val = matrix["A"]["Y"]
+```
 
@@ -57,2 +58,3 @@ ### Custom matrix
 matrix = bl.BLOSUM("path/to/blosum.file")
+val = matrix["A"]["Y"]
 ```
@@ -77,6 +79,12 @@
 ```python
-val = matrix["AY"]
+val = matrix["A"]["Y"]
 ```
+To get a defaultdict of the row with a given key use:
 
-If the key cannot be found, the default value is returned. It is `float("-inf")`.
+```python
+val_dict = matrix["A"]
+```
+
+
+If the key cannot be found, the default value `float("-inf")` is returned.
 It is possible to set a custom default score:
@@ -89,3 +97,3 @@ ```python
 ```
-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
@@ -92,0 +100,0 @@ TLDR:

setup.cfg

 [metadata]
 name = blosum
-version = 1.2.2
+version = 2.0.1
 description = A simple BLOSUM toolbox without dependencies.
@@ -5,0 +5,0 @@ long_description = file: README.md

src/blosum.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: blosum
-Version: 1.2.2
+Version: 2.0.1
 Summary: A simple BLOSUM toolbox without dependencies.
@@ -41,3 +41,3 @@ Home-page: https://github.com/not-a-feature/blosum
 
-`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.
 
@@ -63,3 +63,3 @@
 
-### Default BLOSUM 
+### Default BLOSUM
 This package provides the most commonly used BLOSUM matrices.
@@ -72,3 +72,4 @@ You can choose from BLOSUM 45, 50, 62, 80 and 90.
 matrix = bl.BLOSUM(62)
-``` 
+val = matrix["A"]["Y"]
+```
 
@@ -81,2 +82,3 @@ ### Custom matrix
 matrix = bl.BLOSUM("path/to/blosum.file")
+val = matrix["A"]["Y"]
 ```
@@ -101,6 +103,12 @@
 ```python
-val = matrix["AY"]
+val = matrix["A"]["Y"]
 ```
+To get a defaultdict of the row with a given key use:
 
-If the key cannot be found, the default value is returned. It is `float("-inf")`.
+```python
+val_dict = matrix["A"]
+```
+
+
+If the key cannot be found, the default value `float("-inf")` is returned.
 It is possible to set a custom default score:
@@ -113,3 +121,3 @@ ```python
 ```
-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
@@ -116,0 +124,0 @@ TLDR:

src/blosum.egg-info/SOURCES.txt

@@ -14,2 +14,4 @@ LICENSE
 src/blosum.egg-info/requires.txt
-src/blosum.egg-info/top_level.txt
+src/blosum.egg-info/top_level.txt
+tests/test_blosum.py
+tests/test_loadMatrix.py

src/blosum/_blosum.py

@@ -17,3 +17,3 @@ """
 class BLOSUM(defaultdict):  # type: ignore
-    def __init__(self, n, default: float = float("-inf")):
+    def __init__(self, n: Union[int, str], default: float = float("-inf")):
         """
@@ -23,12 +23,15 @@ Object to easily access a blosum matrix.
 
-        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
         """
@@ -40,8 +43,11 @@
         # 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:
@@ -79,3 +85,6 @@ raise (
 
-def loadMatrix(path: str) -> Union[Dict[str, int], Dict[str, float]]:
+def loadMatrix(
+    path: str,
+    default: float = float("-inf"),
+) -> DefaultDict[str, DefaultDict[str, float]]:
     """
@@ -86,6 +95,9 @@ Reads a Blosum matrix from file.
 
-    Input:
+    Input
+    -----
         path: str, path to a file.
+        default: float, default value "-inf"
 
-    Returns:
+    Returns
+    -------
         blosumDict: Dictionary, The blosum dict
@@ -97,3 +109,5 @@ """
 
-    blosumDict = {}
+    blosumDict: DefaultDict[str, DefaultDict[str, float]] = defaultdict(
+        lambda: defaultdict(lambda: default)
+    )
 
@@ -126,7 +140,8 @@ header = True
         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

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Total package byte prevSize

145431

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Number of package files

17

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Lines of code

4249

31.18%