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blosum
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+104
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| Metadata-Version: 2.1 | ||
| Name: blosum | ||
| Version: 1.1.1 | ||
| Version: 1.1.2 | ||
| Summary: A simple BLOSUM toolbox without dependencies. | ||
@@ -8,101 +8,3 @@ Home-page: https://github.com/not-a-feature/blosum | ||
| License: gpl-3.0 | ||
| Description:  | ||
| A small module for easy access to BLOSUM matrices without dependencies. | ||
|  | ||
|  | ||
|  | ||
| The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between protein sequences and are therefore mainly used in bioinformatics. | ||
| 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. | ||
| ## Installation | ||
| Using pip / pip3: | ||
| ```bash | ||
| pip install blosum | ||
| ``` | ||
| Or by source: | ||
| ```bash | ||
| git clone git@github.com:not-a-feature/blosum.git | ||
| cd blosum | ||
| pip install . | ||
| ``` | ||
| ## How to use | ||
| ### Default BLOSUM | ||
| This package provides with the 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) | ||
| ``` | ||
| ### 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") | ||
| ``` | ||
| The matrices are required to have following format: | ||
| ``` | ||
| # Comments should start with # | ||
| # Each value should be seperated by one or many whitespace | ||
| A R N D | ||
| A 5 -2 -1 -2 | ||
| R -2 7 0 -1 | ||
| N -1 0 6 2 | ||
| D -2 -1 2 7 | ||
| ``` | ||
| ### Getting Values. | ||
| To get a value use: | ||
| ```python | ||
| val = matrix["AY"] | ||
| ``` | ||
| 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")`. | ||
| It is possible to set a custom default score: | ||
| ```python | ||
| matrix = bl.BLOSUM(62, default=0) | ||
| ``` | ||
| ## License | ||
| ``` | ||
| Copyright (C) 2021 by Jules Kreuer - @not_a_feature | ||
| This piece of software is published unter the GNU General Public License v3.0 | ||
| TLDR: | ||
| | Permissions | Conditions | Limitations | | ||
| | ---------------- | ---------------------------- | ----------- | | ||
| | ✓ Commercial use | Disclose source | ✕ Liability | | ||
| | ✓ Distribution | License and copyright notice | ✕ Warranty | | ||
| | ✓ Modification | Same license | | | ||
| | ✓ Patent use | State changes | | | ||
| | ✓ Private use | | | | ||
| ``` | ||
| Go to [LICENSE.md](https://github.com/not-a-feature/blosum/blob/main/LICENSE) to see the full version. | ||
| ## Dependencies | ||
| 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. | ||
| Keywords: BLOSUM,reader,bio,bioinformatics | ||
| Keywords: BLOSUM,reader,bio,bioinformatics,blosum62,blosum45,blosum50,blosum90 | ||
| Platform: unix | ||
@@ -116,4 +18,106 @@ Platform: linux | ||
| Classifier: Programming Language :: Python :: 3.9 | ||
| Classifier: Programming Language :: Python :: 3.10 | ||
| Requires-Python: >=3.8 | ||
| Description-Content-Type: text/markdown | ||
| Provides-Extra: testing | ||
| License-File: LICENSE | ||
|  | ||
| A small module for easy access to BLOSUM matrices without dependencies. | ||
|  | ||
|  | ||
|  | ||
| The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between protein sequences and are therefore mainly used in bioinformatics. | ||
| 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. | ||
| ## Installation | ||
| Using pip / pip3: | ||
| ```bash | ||
| pip install blosum | ||
| ``` | ||
| Or by source: | ||
| ```bash | ||
| git clone git@github.com:not-a-feature/blosum.git | ||
| cd blosum | ||
| pip install . | ||
| ``` | ||
| ## How to use | ||
| ### 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) | ||
| ``` | ||
| ### 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") | ||
| ``` | ||
| The matrices are required to have following format: | ||
| ``` | ||
| # Comments should start with # | ||
| # Each value should be seperated by one or many whitespace | ||
| A R N D | ||
| A 5 -2 -1 -2 | ||
| R -2 7 0 -1 | ||
| N -1 0 6 2 | ||
| D -2 -1 2 7 | ||
| ``` | ||
| ### Getting Values. | ||
| To get a value use: | ||
| ```python | ||
| val = matrix["AY"] | ||
| ``` | ||
| 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")`. | ||
| It is possible to set a custom default score: | ||
| ```python | ||
| matrix = bl.BLOSUM(62, default=0) | ||
| ``` | ||
| ## License | ||
| ``` | ||
| Copyright (C) 2021 by Jules Kreuer - @not_a_feature | ||
| This piece of software is published unter the GNU General Public License v3.0 | ||
| TLDR: | ||
| | Permissions | Conditions | Limitations | | ||
| | ---------------- | ---------------------------- | ----------- | | ||
| | ✓ Commercial use | Disclose source | ✕ Liability | | ||
| | ✓ Distribution | License and copyright notice | ✕ Warranty | | ||
| | ✓ Modification | Same license | | | ||
| | ✓ Patent use | State changes | | | ||
| | ✓ Private use | | | | ||
| ``` | ||
| Go to [LICENSE.md](https://github.com/not-a-feature/blosum/blob/main/LICENSE) to see the full version. | ||
| ## Dependencies | ||
| 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. | ||
+1
-1
@@ -32,3 +32,3 @@  | ||
| ### Default BLOSUM | ||
| This package provides with the commonly used BLOSUM matrices. | ||
| This package provides the most commonly used BLOSUM matrices. | ||
| You can choose from BLOSUM 45, 50, 62, 80 and 90. | ||
@@ -35,0 +35,0 @@ |
+3
-2
| [metadata] | ||
| name = blosum | ||
| version = 1.1.1 | ||
| version = 1.1.2 | ||
| description = A simple BLOSUM toolbox without dependencies. | ||
| long_description = file: README.md | ||
| long_description_content_type = text/markdown | ||
| keywords = BLOSUM, reader, bio, bioinformatics | ||
| keywords = BLOSUM, reader, bio, bioinformatics, blosum62, blosum45, blosum50, blosum90 | ||
| home-page = https://github.com/not-a-feature/blosum | ||
@@ -17,2 +17,3 @@ author = Jules Kreuer / not_a_feature | ||
| Programming Language :: Python :: 3.9 | ||
| Programming Language :: Python :: 3.10 | ||
@@ -19,0 +20,0 @@ [options] |
+104
-100
| Metadata-Version: 2.1 | ||
| Name: blosum | ||
| Version: 1.1.1 | ||
| Version: 1.1.2 | ||
| Summary: A simple BLOSUM toolbox without dependencies. | ||
@@ -8,101 +8,3 @@ Home-page: https://github.com/not-a-feature/blosum | ||
| License: gpl-3.0 | ||
| Description:  | ||
| A small module for easy access to BLOSUM matrices without dependencies. | ||
|  | ||
|  | ||
|  | ||
| The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between protein sequences and are therefore mainly used in bioinformatics. | ||
| 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. | ||
| ## Installation | ||
| Using pip / pip3: | ||
| ```bash | ||
| pip install blosum | ||
| ``` | ||
| Or by source: | ||
| ```bash | ||
| git clone git@github.com:not-a-feature/blosum.git | ||
| cd blosum | ||
| pip install . | ||
| ``` | ||
| ## How to use | ||
| ### Default BLOSUM | ||
| This package provides with the 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) | ||
| ``` | ||
| ### 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") | ||
| ``` | ||
| The matrices are required to have following format: | ||
| ``` | ||
| # Comments should start with # | ||
| # Each value should be seperated by one or many whitespace | ||
| A R N D | ||
| A 5 -2 -1 -2 | ||
| R -2 7 0 -1 | ||
| N -1 0 6 2 | ||
| D -2 -1 2 7 | ||
| ``` | ||
| ### Getting Values. | ||
| To get a value use: | ||
| ```python | ||
| val = matrix["AY"] | ||
| ``` | ||
| 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")`. | ||
| It is possible to set a custom default score: | ||
| ```python | ||
| matrix = bl.BLOSUM(62, default=0) | ||
| ``` | ||
| ## License | ||
| ``` | ||
| Copyright (C) 2021 by Jules Kreuer - @not_a_feature | ||
| This piece of software is published unter the GNU General Public License v3.0 | ||
| TLDR: | ||
| | Permissions | Conditions | Limitations | | ||
| | ---------------- | ---------------------------- | ----------- | | ||
| | ✓ Commercial use | Disclose source | ✕ Liability | | ||
| | ✓ Distribution | License and copyright notice | ✕ Warranty | | ||
| | ✓ Modification | Same license | | | ||
| | ✓ Patent use | State changes | | | ||
| | ✓ Private use | | | | ||
| ``` | ||
| Go to [LICENSE.md](https://github.com/not-a-feature/blosum/blob/main/LICENSE) to see the full version. | ||
| ## Dependencies | ||
| 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. | ||
| Keywords: BLOSUM,reader,bio,bioinformatics | ||
| Keywords: BLOSUM,reader,bio,bioinformatics,blosum62,blosum45,blosum50,blosum90 | ||
| Platform: unix | ||
@@ -116,4 +18,106 @@ Platform: linux | ||
| Classifier: Programming Language :: Python :: 3.9 | ||
| Classifier: Programming Language :: Python :: 3.10 | ||
| Requires-Python: >=3.8 | ||
| Description-Content-Type: text/markdown | ||
| Provides-Extra: testing | ||
| License-File: LICENSE | ||
|  | ||
| A small module for easy access to BLOSUM matrices without dependencies. | ||
|  | ||
|  | ||
|  | ||
| The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between protein sequences and are therefore mainly used in bioinformatics. | ||
| 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. | ||
| ## Installation | ||
| Using pip / pip3: | ||
| ```bash | ||
| pip install blosum | ||
| ``` | ||
| Or by source: | ||
| ```bash | ||
| git clone git@github.com:not-a-feature/blosum.git | ||
| cd blosum | ||
| pip install . | ||
| ``` | ||
| ## How to use | ||
| ### 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) | ||
| ``` | ||
| ### 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") | ||
| ``` | ||
| The matrices are required to have following format: | ||
| ``` | ||
| # Comments should start with # | ||
| # Each value should be seperated by one or many whitespace | ||
| A R N D | ||
| A 5 -2 -1 -2 | ||
| R -2 7 0 -1 | ||
| N -1 0 6 2 | ||
| D -2 -1 2 7 | ||
| ``` | ||
| ### Getting Values. | ||
| To get a value use: | ||
| ```python | ||
| val = matrix["AY"] | ||
| ``` | ||
| 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")`. | ||
| It is possible to set a custom default score: | ||
| ```python | ||
| matrix = bl.BLOSUM(62, default=0) | ||
| ``` | ||
| ## License | ||
| ``` | ||
| Copyright (C) 2021 by Jules Kreuer - @not_a_feature | ||
| This piece of software is published unter the GNU General Public License v3.0 | ||
| TLDR: | ||
| | Permissions | Conditions | Limitations | | ||
| | ---------------- | ---------------------------- | ----------- | | ||
| | ✓ Commercial use | Disclose source | ✕ Liability | | ||
| | ✓ Distribution | License and copyright notice | ✕ Warranty | | ||
| | ✓ Modification | Same license | | | ||
| | ✓ Patent use | State changes | | | ||
| | ✓ Private use | | | | ||
| ``` | ||
| Go to [LICENSE.md](https://github.com/not-a-feature/blosum/blob/main/LICENSE) to see the full version. | ||
| ## Dependencies | ||
| 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. | ||
| [testing] | ||
| pytest>=6.0 | ||
| pytest-cov>=2.0 | ||
| flake8>=3.9 | ||
| pytest-cov>=2.0 | ||
| pytest>=6.0 | ||
| tox>=3.20 |
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