| Name | antpack JSON |
| Version |
0.4
JSON |
| download |
| home_page | None |
| Summary | A Python package for processing, manipulating and making inferences about antibody sequence data |
| upload_time | 2025-08-06 00:50:33 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | Academic Software Licence (“ASL”) Preamble ASL is a software license that proposes to offer copyleft style rights to use the software in an academic non-commercial setting. The purpose of ASL is to encourage academic cooperation and collaboration free-of-charge whilst enabling academic institutions to earn revenue from the parallel licensing of valuable bodies of software code. Significant proportions of such revenue are typically reinvested in academic research. ASL is not an open-source licence because it does not allow commercial use – it is an “available source” licence, meaning that the source code is made available subject to the terms of this licence and only for academic non-commercial use. ASL is a reciprocal licence very similar to GPL and the core terms are identical to those of GNU GPLv2 (except for the limitation to non-commercial use), making it easier for those who know the GPLv2 to understand the licensing*. As a reciprocal licence, if you redistribute any derivative works you have created based on ASL licenced code, then you are required to license the new work under the ASL - including making your source code available and ensuring that licensees are aware of the terms of the ASL licence. The non-commercial limitation makes ASL incompatible with the GPL and other open-source licences with copyleft provisions because these licences require that modified versions of the original program are made available free of charge for any type of use, including commercial, and this is prevented by ASL. As the two sets of reciprocal terms are incompatible, any modified version of the original program combining ASL and copylefted open-source code can be used internally but cannot be licensed out. The non-commercial restriction is an integral part of the license and you may not remove it without the consent of the rights holder in the ASL licensed code. Please contact Cambridge Enterprise for any questions and/or to enquire about commercial use rights. *The changes to the GPLv2 are: removing the Preamble, replacing the reference to the “General Public License” in clause 0 with a reference to the “ASL”, removing clause 9 and adding clause 13 with the non-commercial restriction and limited patent grant TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 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| keywords |
antibody
antibodies
antibody numbering
antibody humanization
antibody humanness
antibody analysis
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# AntPack

AntPack is a Python package / toolkit for antibody numbering, data processing,
statistical inference and machine learning for antibody sequences and TCRs.
It is currently in active development, so we are adding new features
and making more improvements periodically.
## Usage
For usage for v0.3.9 and later, see the [docs at this link.](https://antpackdocumentationlatest.pages.dev/)
[You can find the docs here for older versions.](https://antpackdocumentation.pages.dev/)
## What's new in v0.4
v0.4 contains a bug fix for VJ gene assignment for numbering schemes
*other* than IMGT. If perforiming VJ gene assignment with numbering
schemes *other* than IMGT, please prefer v0.4 to prior versions.
The API for the SequenceScoringTool and humanization has been updated
and streamlined so if you are scoring sequences for humanness or
humanizing them please see the updated section of the docs.
v0.4 also contains capabilities for clustering antibody datasets
ranging in size from a few dozen sequences to tens of millions
using a variety of algorithms using any CDR or framework region
of interest. (see below and see docs). These will be significantly
expanded in the next version with further clustering and search
capabilities and structure analysis-related tools.
## Licensing
Versions v0.3.9 and afterwards are licensed for academic and noncommercial
use only; you must first obtain a [free license key](https://pwslicensekey.pythonanywhere.com/)
to use. You do not have to re-setup the key when upgrading AntPack in
an existing venv or conda environment.
Versions prior to 0.3.9 were made available under the GPL, which means they
can be used it for your own data analysis in any manner you wish
whether you work in academia or industry,
but any software built using AntPack and intended for sale or distribution
must also be open-source under the GPL license. Therefore if
you are currently using e.g. v0.3.8.5 for data analysis,
you should feel free to continue to do so under the
terms of your existing license. Also note that v0.3.8.5 is still
available on PyPi and can be installed using:
```
pip install antpack==0.3.8.5
```
## Installation
Starting with v0.3.9, AntPack is only available for noncommercial
academic use. To use AntPack versions
v0.3.9 or later, you must first obtain a [free license key](https://pwslicensekey.pythonanywhere.com/).
To install AntPack, run:
```
pip install antpack
AntPack-setup
```
then paste in the license key and your email address when prompted.
The only required dependency is numpy. If you want to run the GUI,
there are two additional dependencies you'll need to install:
```
pip install pyside6 qt_material
```
If you don't plan to use the GUI, you don't need those dependencies.
AntPack is distributed as a wheel precompiled for most platforms and CPython >= 3.8.
## Capabilities
#### Antibody numbering
Numbering antibody sequences is an important precursor for many statistical inference /
machine learning applications. AntPack is orders of magnitude faster for numbering
antibody sequences than existing tools in the literature (e.g. ANARCI, AbRSA),
while providing >= reliability. AntPack also provides tools for merging a list
of numbered sequences into an MSA, for easy extraction of specific CDRs and
framework regions, and for TCR numbering.
#### V / J genes
Identifying the most similar human/mouse/llama/rabbit V / J gene sequences is useful
for a variety of purposes. AntPack provides tools for determining which human
V and J gene sequences are most similar to the variable region chain provided
as input.
#### Humanness and developability
Minimizing the risk of immunogenicity is important for selecting clinical
candidates. In AntPack v0.1.0, we introduce a simple, fully interpretable
generative model for human heavy and light chains that outperforms all
comparators in the literature on a large held-out test set for distinguishing
human sequences from those of other species. This scoring tool can be used
to score sequences for humanness, suggest modifications to make them more
human, identify liabilities, and generate highly human sequences that contain
selected motifs.
#### Finding developability liabilities
Some sequence motifs are known to be associated with developability issues -- certain
motifs are known, for example, to be prone to N-glycosylation or deamidation. AntPack
provides a tool for finding these "liability" motifs in an input sequence. Note that
that identifying liabilities through finding motifs in this way is known to be prone
to false positives (an N-glycosylation motif, for example, will not always be glycosylated).
Still, these kinds of alerts can be useful for making yourself aware of potential
developability issues.
### Clustering
 Starting in v0.4,
AntPack contains tools for quickly clustering both small and large sequence
datasets using all or part of the antibody sequence.
### Citing this work
If using AntPack in research intended for publication, please cite
either the preprint:
Jonathan Parkinson and Wei Wang. 2024. For antibody sequence generative modeling,
mixture models may be all you need.
[bioRxiv: https://doi.org/10.1101/2024.01.27.577555](https://www.biorxiv.org/content/10.1101/2024.01.27.577555v1)
or the final paper in [Bioinformatics.](https://academic.oup.com/bioinformatics/article/40/5/btae278/7656770)
#### Acknowledgements
The authors & maintainers gratefully acknowledge the contributions of
Japanese artist Yusuke Kamiyamane for the creation of the Fugue icon set.
Raw data
{
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"home_page": null,
"name": "antpack",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": null,
"keywords": "antibody, antibodies, antibody numbering, antibody humanization, antibody humanness, antibody analysis",
"author": null,
"author_email": "Jonathan Parkinson <jlparkinson1@gmail.com>",
"download_url": null,
"platform": null,
"description": "# AntPack\n\n\n\nAntPack is a Python package / toolkit for antibody numbering, data processing,\nstatistical inference and machine learning for antibody sequences and TCRs.\nIt is currently in active development, so we are adding new features\nand making more improvements periodically.\n\n## Usage\n\nFor usage for v0.3.9 and later, see the [docs at this link.](https://antpackdocumentationlatest.pages.dev/)\n\n[You can find the docs here for older versions.](https://antpackdocumentation.pages.dev/)\n\n## What's new in v0.4\n\nv0.4 contains a bug fix for VJ gene assignment for numbering schemes\n*other* than IMGT. If perforiming VJ gene assignment with numbering\nschemes *other* than IMGT, please prefer v0.4 to prior versions.\nThe API for the SequenceScoringTool and humanization has been updated\nand streamlined so if you are scoring sequences for humanness or\nhumanizing them please see the updated section of the docs.\n\nv0.4 also contains capabilities for clustering antibody datasets\nranging in size from a few dozen sequences to tens of millions\nusing a variety of algorithms using any CDR or framework region\nof interest. (see below and see docs). These will be significantly\nexpanded in the next version with further clustering and search\ncapabilities and structure analysis-related tools.\n\n## Licensing\n\nVersions v0.3.9 and afterwards are licensed for academic and noncommercial\nuse only; you must first obtain a [free license key](https://pwslicensekey.pythonanywhere.com/)\nto use. You do not have to re-setup the key when upgrading AntPack in\nan existing venv or conda environment.\n\nVersions prior to 0.3.9 were made available under the GPL, which means they\ncan be used it for your own data analysis in any manner you wish\nwhether you work in academia or industry,\nbut any software built using AntPack and intended for sale or distribution \nmust also be open-source under the GPL license. Therefore if\nyou are currently using e.g. v0.3.8.5 for data analysis,\nyou should feel free to continue to do so under the\nterms of your existing license. Also note that v0.3.8.5 is still\navailable on PyPi and can be installed using:\n```\npip install antpack==0.3.8.5\n```\n\n## Installation\n\nStarting with v0.3.9, AntPack is only available for noncommercial\nacademic use. To use AntPack versions\nv0.3.9 or later, you must first obtain a [free license key](https://pwslicensekey.pythonanywhere.com/).\nTo install AntPack, run:\n```\npip install antpack\nAntPack-setup\n```\n\nthen paste in the license key and your email address when prompted.\n\nThe only required dependency is numpy. If you want to run the GUI,\nthere are two additional dependencies you'll need to install:\n```\npip install pyside6 qt_material\n```\n\nIf you don't plan to use the GUI, you don't need those dependencies.\n\nAntPack is distributed as a wheel precompiled for most platforms and CPython >= 3.8.\n\n## Capabilities\n\n\n#### Antibody numbering\n\nNumbering antibody sequences is an important precursor for many statistical inference /\nmachine learning applications. AntPack is orders of magnitude faster for numbering\nantibody sequences than existing tools in the literature (e.g. ANARCI, AbRSA),\nwhile providing >= reliability. AntPack also provides tools for merging a list\nof numbered sequences into an MSA, for easy extraction of specific CDRs and\nframework regions, and for TCR numbering.\n\n\n#### V / J genes\n\nIdentifying the most similar human/mouse/llama/rabbit V / J gene sequences is useful\nfor a variety of purposes. AntPack provides tools for determining which human\nV and J gene sequences are most similar to the variable region chain provided\nas input.\n\n\n#### Humanness and developability\n\nMinimizing the risk of immunogenicity is important for selecting clinical\ncandidates. In AntPack v0.1.0, we introduce a simple, fully interpretable\ngenerative model for human heavy and light chains that outperforms all\ncomparators in the literature on a large held-out test set for distinguishing\nhuman sequences from those of other species. This scoring tool can be used\nto score sequences for humanness, suggest modifications to make them more\nhuman, identify liabilities, and generate highly human sequences that contain\nselected motifs.\n\n\n#### Finding developability liabilities\n\nSome sequence motifs are known to be associated with developability issues -- certain\nmotifs are known, for example, to be prone to N-glycosylation or deamidation. AntPack\nprovides a tool for finding these \"liability\" motifs in an input sequence. Note that\nthat identifying liabilities through finding motifs in this way is known to be prone\nto false positives (an N-glycosylation motif, for example, will not always be glycosylated).\nStill, these kinds of alerts can be useful for making yourself aware of potential\ndevelopability issues.\n\n### Clustering\n\n Starting in v0.4,\nAntPack contains tools for quickly clustering both small and large sequence\ndatasets using all or part of the antibody sequence.\n\n\n### Citing this work\n\nIf using AntPack in research intended for publication, please cite\neither the preprint:\n\nJonathan Parkinson and Wei Wang. 2024. For antibody sequence generative modeling,\nmixture models may be all you need.\n[bioRxiv: https://doi.org/10.1101/2024.01.27.577555](https://www.biorxiv.org/content/10.1101/2024.01.27.577555v1)\n\nor the final paper in [Bioinformatics.](https://academic.oup.com/bioinformatics/article/40/5/btae278/7656770)\n\n#### Acknowledgements\n\nThe authors & maintainers gratefully acknowledge the contributions of\nJapanese artist Yusuke Kamiyamane for the creation of the Fugue icon set.\n",
"bugtrack_url": null,
"license": "Academic Software Licence (\u201cASL\u201d) Preamble ASL is a software license that proposes to offer copyleft style rights to use the software in an academic non-commercial setting. The purpose of ASL is to encourage academic cooperation and collaboration free-of-charge whilst enabling academic institutions to earn revenue from the parallel licensing of valuable bodies of software code. Significant proportions of such revenue are typically reinvested in academic research. ASL is not an open-source licence because it does not allow commercial use \u2013 it is an \u201cavailable source\u201d licence, meaning that the source code is made available subject to the terms of this licence and only for academic non-commercial use. ASL is a reciprocal licence very similar to GPL and the core terms are identical to those of GNU GPLv2 (except for the limitation to non-commercial use), making it easier for those who know the GPLv2 to understand the licensing*. As a reciprocal licence, if you redistribute any derivative works you have created based on ASL licenced code, then you are required to license the new work under the ASL - including making your source code available and ensuring that licensees are aware of the terms of the ASL licence. The non-commercial limitation makes ASL incompatible with the GPL and other open-source licences with copyleft provisions because these licences require that modified versions of the original program are made available free of charge for any type of use, including commercial, and this is prevented by ASL. As the two sets of reciprocal terms are incompatible, any modified version of the original program combining ASL and copylefted open-source code can be used internally but cannot be licensed out. The non-commercial restriction is an integral part of the license and you may not remove it without the consent of the rights holder in the ASL licensed code. Please contact Cambridge Enterprise for any questions and/or to enquire about commercial use rights. *The changes to the GPLv2 are: removing the Preamble, replacing the reference to the \u201cGeneral Public License\u201d in clause 0 with a reference to the \u201cASL\u201d, removing clause 9 and adding clause 13 with the non-commercial restriction and limited patent grant TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this License. The \"Program\", below, refers to any such program or work, and a \"work based on the Program\" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term \"modification\".) Each licensee is addressed as \"you\". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 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