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blosum
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blosum - npm Package Compare versions
+11
-11
| Metadata-Version: 2.1 | ||
| Name: blosum | ||
| Version: 1.1.3 | ||
| Version: 1.2.0 | ||
| Summary: A simple BLOSUM toolbox without dependencies. | ||
@@ -15,6 +15,7 @@ Home-page: https://github.com/not-a-feature/blosum | ||
| Classifier: Programming Language :: Python :: 3 | ||
| Classifier: Programming Language :: Python :: 3.7 | ||
| Classifier: Programming Language :: Python :: 3.8 | ||
| Classifier: Programming Language :: Python :: 3.9 | ||
| Classifier: Programming Language :: Python :: 3.10 | ||
| Requires-Python: >=3.8 | ||
| Requires-Python: >=3.7 | ||
| Description-Content-Type: text/markdown | ||
@@ -31,2 +32,3 @@ Provides-Extra: testing | ||
|  | ||
| [](http://bioconda.github.io/recipes/blosum/README.html) | ||
| [](https://github.com/psf/black) | ||
@@ -54,2 +56,6 @@ | ||
| Or by conda: | ||
| ```bash | ||
| conda install blosum | ||
| ``` | ||
| ## How to use | ||
@@ -67,3 +73,3 @@ | ||
| ### Custom Matrix | ||
| ### Custom matrix | ||
| In addition, own matrices can be loaded. For this, the path is given as an argument. | ||
@@ -88,3 +94,4 @@ | ||
| ### Getting Values. | ||
| ### Getting values: | ||
| Once loaded the `matrix` behaves like a `defaultdict`. | ||
| To get a value use: | ||
@@ -96,8 +103,2 @@ | ||
| Or get the dictionary representation of the BLOSUM matrix. | ||
| ```python | ||
| blosum_dict = dict(matrix) | ||
| ``` | ||
| If the key cannot be found, the default value is returned. It is `float("-inf")`. | ||
@@ -128,2 +129,1 @@ It is possible to set a custom default score: | ||
| Go to [DEPENDENCIES.md](https://github.com/not-a-feature/blosum/blob/main/DEPENDENCIES.md) to see all dependencies and licenses. | ||
+9
-9
@@ -8,2 +8,3 @@  | ||
|  | ||
| [](http://bioconda.github.io/recipes/blosum/README.html) | ||
| [](https://github.com/psf/black) | ||
@@ -31,2 +32,6 @@ | ||
| Or by conda: | ||
| ```bash | ||
| conda install blosum | ||
| ``` | ||
| ## How to use | ||
@@ -44,3 +49,3 @@ | ||
| ### Custom Matrix | ||
| ### Custom matrix | ||
| In addition, own matrices can be loaded. For this, the path is given as an argument. | ||
@@ -65,3 +70,4 @@ | ||
| ### Getting Values. | ||
| ### Getting values: | ||
| Once loaded the `matrix` behaves like a `defaultdict`. | ||
| To get a value use: | ||
@@ -73,8 +79,2 @@ | ||
| Or get the dictionary representation of the BLOSUM matrix. | ||
| ```python | ||
| blosum_dict = dict(matrix) | ||
| ``` | ||
| If the key cannot be found, the default value is returned. It is `float("-inf")`. | ||
@@ -104,2 +104,2 @@ It is possible to set a custom default score: | ||
| In addition to packages included in Python 3, this piece of software uses 3rd-party software packages for development purposes that are not required in the published version. | ||
| Go to [DEPENDENCIES.md](https://github.com/not-a-feature/blosum/blob/main/DEPENDENCIES.md) to see all dependencies and licenses. | ||
| Go to [DEPENDENCIES.md](https://github.com/not-a-feature/blosum/blob/main/DEPENDENCIES.md) to see all dependencies and licenses. |
+3
-2
| [metadata] | ||
| name = blosum | ||
| version = 1.1.3 | ||
| version = 1.2.0 | ||
| description = A simple BLOSUM toolbox without dependencies. | ||
@@ -15,2 +15,3 @@ long_description = file: README.md | ||
| Programming Language :: Python :: 3 | ||
| Programming Language :: Python :: 3.7 | ||
| Programming Language :: Python :: 3.8 | ||
@@ -23,3 +24,3 @@ Programming Language :: Python :: 3.9 | ||
| blosum | ||
| python_requires = >=3.8 | ||
| python_requires = >=3.7 | ||
| package_dir = | ||
@@ -26,0 +27,0 @@ =src |
| Metadata-Version: 2.1 | ||
| Name: blosum | ||
| Version: 1.1.3 | ||
| Version: 1.2.0 | ||
| Summary: A simple BLOSUM toolbox without dependencies. | ||
@@ -15,6 +15,7 @@ Home-page: https://github.com/not-a-feature/blosum | ||
| Classifier: Programming Language :: Python :: 3 | ||
| Classifier: Programming Language :: Python :: 3.7 | ||
| Classifier: Programming Language :: Python :: 3.8 | ||
| Classifier: Programming Language :: Python :: 3.9 | ||
| Classifier: Programming Language :: Python :: 3.10 | ||
| Requires-Python: >=3.8 | ||
| Requires-Python: >=3.7 | ||
| Description-Content-Type: text/markdown | ||
@@ -31,2 +32,3 @@ Provides-Extra: testing | ||
|  | ||
| [](http://bioconda.github.io/recipes/blosum/README.html) | ||
| [](https://github.com/psf/black) | ||
@@ -54,2 +56,6 @@ | ||
| Or by conda: | ||
| ```bash | ||
| conda install blosum | ||
| ``` | ||
| ## How to use | ||
@@ -67,3 +73,3 @@ | ||
| ### Custom Matrix | ||
| ### Custom matrix | ||
| In addition, own matrices can be loaded. For this, the path is given as an argument. | ||
@@ -88,3 +94,4 @@ | ||
| ### Getting Values. | ||
| ### Getting values: | ||
| Once loaded the `matrix` behaves like a `defaultdict`. | ||
| To get a value use: | ||
@@ -96,8 +103,2 @@ | ||
| Or get the dictionary representation of the BLOSUM matrix. | ||
| ```python | ||
| blosum_dict = dict(matrix) | ||
| ``` | ||
| If the key cannot be found, the default value is returned. It is `float("-inf")`. | ||
@@ -128,2 +129,1 @@ It is possible to set a custom default score: | ||
| Go to [DEPENDENCIES.md](https://github.com/not-a-feature/blosum/blob/main/DEPENDENCIES.md) to see all dependencies and licenses. | ||
@@ -1,5 +0,3 @@ | ||
| from ._blosum import BLOSUM | ||
| from ._blosum import BLOSUM, loadMatrix | ||
| __all__ = [ | ||
| "BLOSUM", | ||
| ] | ||
| __all__ = ["BLOSUM", "loadMatrix"] |
+67
-77
@@ -12,5 +12,7 @@ """ | ||
| from ._data import default_blosum | ||
| from collections import defaultdict | ||
| from typing import Dict, Union, DefaultDict | ||
| class BLOSUM: | ||
| class BLOSUM(defaultdict): # type: ignore | ||
| def __init__(self, n, default: float = float("-inf")): | ||
@@ -38,100 +40,88 @@ """ | ||
| if n in [45, 50, 62, 80, 90]: | ||
| self.matrix = default_blosum[n] | ||
| super().__init__(lambda: default, default_blosum[n]) | ||
| # load custom matrix | ||
| elif isinstance(n, str): | ||
| # load custom matrix | ||
| self.__loadMatrix(n) | ||
| super().__init__(lambda: default, loadMatrix(n)) | ||
| else: | ||
| raise (BaseException("Can't initate empty BLOSUM Object")) | ||
| raise ( | ||
| BaseException( | ||
| f"""Unknown BLOSUM Number '{n}'. Choose n ϵ {{45,50,62,80,90}} or provide a path to a matrix.""" | ||
| ) | ||
| ) | ||
| def __loadMatrix(self, path: str) -> None: | ||
| def __str__(self) -> str: | ||
| """ | ||
| 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 | ||
| Magic method to allow BLOSUM object printing. | ||
| """ | ||
| return f"BLOSUM({self.n}, default={self.default}, {dict(self)}" | ||
| Input: | ||
| path: str, path to a file. | ||
| Returns: | ||
| blosumDict: Dictionary, Blosum-Dict | ||
| def __repr__(self) -> str: | ||
| """ | ||
| Magic method to allow printing of the BLOSUM representation. | ||
| """ | ||
| if self.default == float("-inf"): | ||
| d = "float('-inf')" | ||
| elif self.default == float("inf"): | ||
| d = "float('inf')" | ||
| else: | ||
| d = str(self.default) | ||
| with open(path, "r") as f: | ||
| content = f.readlines() | ||
| if self.n in [45, 50, 62, 80, 90]: | ||
| n = self.n | ||
| else: | ||
| n = f'"{self.n}"' | ||
| blosumDict = {} | ||
| return f"BLOSUM({n}, default={d})" | ||
| header = True | ||
| for line in content: | ||
| line = line.strip() | ||
| # Skip comments starting with # | ||
| if line.startswith("#"): | ||
| continue | ||
| def loadMatrix(path: str) -> Union[Dict[str, int], Dict[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 | ||
| linelist = line.split() | ||
| Input: | ||
| path: str, path to a file. | ||
| # Extract labels only once | ||
| if header: | ||
| labelslist = linelist | ||
| header = False | ||
| Returns: | ||
| blosumDict: Dictionary, The blosum dict | ||
| """ | ||
| # Check if all AA are covered | ||
| if not len(labelslist) == 25: | ||
| warn(UserWarning("Blosum matrix may not cover all amino-acids")) | ||
| continue | ||
| with open(path, "r") as f: | ||
| content = f.readlines() | ||
| if not len(linelist) == len(labelslist) + 1: | ||
| # Check if line has as may entries as labels | ||
| raise EOFError("Blosum file is missing values.") | ||
| blosumDict = {} | ||
| # Add Line/Label combination to dict | ||
| for index, lab in enumerate(labelslist, start=1): | ||
| blosumDict[f"{linelist[0]}{lab}"] = float(linelist[index]) | ||
| header = True | ||
| for line in content: | ||
| line = line.strip() | ||
| # Check quadratic | ||
| if not len(blosumDict) == len(labelslist) ** 2: | ||
| raise EOFError("Blosum file is not quadratic.") | ||
| self.matrix = blosumDict | ||
| # Skip comments starting with # | ||
| if line.startswith("#"): | ||
| continue | ||
| def keys(self): | ||
| """ | ||
| Returns the keys of the blosum matrix | ||
| """ | ||
| return self.matrix.keys() | ||
| linelist = line.split() | ||
| def __getitem__(self, key: str) -> float: | ||
| """ | ||
| Magic method to get the BLOSUM score. | ||
| # Extract labels only once | ||
| if header: | ||
| labelslist = linelist | ||
| header = False | ||
| Input: | ||
| key: String, Combination of both amino-acids. | ||
| Ouput: | ||
| score: Float, value or default value.isinstance(self.n, ) | ||
| """ | ||
| # Check if all AA are covered | ||
| if not len(labelslist) == 25: | ||
| warn(UserWarning("Blosum matrix may not cover all amino-acids")) | ||
| continue | ||
| try: | ||
| score = self.matrix[key] | ||
| except KeyError: | ||
| score = self.default | ||
| if not len(linelist) == len(labelslist) + 1: | ||
| # Check if line has as may entries as labels | ||
| raise EOFError("Blosum file is missing values.") | ||
| return score | ||
| # Add Line/Label combination to dict | ||
| for index, lab in enumerate(labelslist, start=1): | ||
| blosumDict[f"{linelist[0]}{lab}"] = float(linelist[index]) | ||
| def __str__(self) -> str: | ||
| """ | ||
| Magic method to allow BLOSUM object printing. | ||
| """ | ||
| return f"BLOSUM {self.n}\n{self.matrix}" | ||
| def __repr__(self) -> str: | ||
| """ | ||
| Magic method to allow printing of the BLOSUM representation. | ||
| """ | ||
| d = "float('-inf')" if self.default == float("-inf") else self.default | ||
| if self.n in [45, 50, 62, 80, 90]: | ||
| n = self.n | ||
| else: | ||
| n = f'"{self.n}"' | ||
| return f"BLOSUM({n}, default={d})" | ||
| # Check quadratic | ||
| if not len(blosumDict) == len(labelslist) ** 2: | ||
| raise EOFError("Blosum file is not quadratic.") | ||
| return blosumDict |
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Improved metrics
- Total package byte prevSize
113979
0.36%Worsened metrics
- Lines of code
3239
-0.28%