| Name | vectome JSON |
| Version |
0.0.3
JSON |
| download |
| home_page | None |
| Summary | Deterministic vectorization of genomes. |
| upload_time | 2025-10-19 22:20:13 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | MIT License
Copyright (c) [year] [fullname]
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE. |
| keywords |
template
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
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|
# 🧬 vectome
**vectome** is a python package for deterministic vectorization of genomes.
- [Installation](#installation)
- [Command-line interface](#command-line-interface)
- [Issues, problems, suggestions](#issues-problems-suggestions)
- [Documentation](#documentation)
## Installation
### The easy way
You can install the precompiled version directly using `pip`.
```bash
$ pip install vectome
```
### From source
Clone the repository, then `cd` into it. Then run:
```bash
$ pip install -e .
```
## Command-line interface
**vectome** has a command-line interface.
```bash
$ vectome --help
```
You can generate vector embeddings by species / strain name or taxon ID.
```bash
$ vectome embed <(printf "Mycobacterium tuberculosis\n83333\nEscherichia coli CFT073")
```
The resulting vectors are based on MinHash sketches from [sourmash](), then folded into a 4096-vector using
the CountSketch method. You can make a shorter vector using e.g. `-n 1024`.
You can also deterministically project into a dense vector.
```bash
$ vectome embed <(printf "Mycobacterium tuberculosis H37Rv") --projection 16
```
Change the seed with e.g. `--seed 0`.
If you need a more interpretable vector, you can generate one based on Jaccard distances to
landmark species.
```bash
$ vectome embed <(printf "Mycobacterium tuberculosis H37Rv") --method landmark
```
Several landmark groups are available. You can set the group with `--group 0`, and
get information about each one with `vectome info`.
```bash
$ vectome info
vectome version 0.0.1:
group-0: {'landmarks': 113, 'manifest file': '.../vectome/vectome/data/landmarks/group-0/manifest.json', 'built': True}
group-1: {'landmarks': 4, 'manifest file': '.../vectome/vectome/data/landmarks/group-1/manifest.json', 'built': True}
group-2: {'landmarks': 1, 'manifest file': '.../vectome/vectome/data/landmarks/group-2/manifest.json', 'built': False}
meta: {'cache location': '.../vectome/vectome/data/landmarks', 'cache exists': True}
```
## Issues, problems, suggestions
Add to the [issue tracker](https://www.github.com/scbirlab/vectome/issues).
## Documentation
(To come at [ReadTheDocs](https://vectome.readthedocs.org).)
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"description": "# \ud83e\uddec vectome\n\n\n\n\n\n**vectome** is a python package for deterministic vectorization of genomes. \n\n- [Installation](#installation)\n- [Command-line interface](#command-line-interface)\n- [Issues, problems, suggestions](#issues-problems-suggestions)\n- [Documentation](#documentation)\n\n## Installation\n\n### The easy way\n\nYou can install the precompiled version directly using `pip`.\n\n```bash\n$ pip install vectome\n```\n\n### From source\n\nClone the repository, then `cd` into it. Then run:\n\n```bash\n$ pip install -e .\n```\n\n## Command-line interface\n\n**vectome** has a command-line interface. \n\n```bash\n$ vectome --help\n```\n\nYou can generate vector embeddings by species / strain name or taxon ID.\n\n```bash\n$ vectome embed <(printf \"Mycobacterium tuberculosis\\n83333\\nEscherichia coli CFT073\")\n```\n\nThe resulting vectors are based on MinHash sketches from [sourmash](), then folded into a 4096-vector using\nthe CountSketch method. You can make a shorter vector using e.g. `-n 1024`.\n\nYou can also deterministically project into a dense vector.\n\n```bash\n$ vectome embed <(printf \"Mycobacterium tuberculosis H37Rv\") --projection 16\n```\n\nChange the seed with e.g. `--seed 0`.\n\nIf you need a more interpretable vector, you can generate one based on Jaccard distances to\nlandmark species.\n\n```bash\n$ vectome embed <(printf \"Mycobacterium tuberculosis H37Rv\") --method landmark\n```\n\nSeveral landmark groups are available. You can set the group with `--group 0`, and \nget information about each one with `vectome info`.\n\n```bash\n$ vectome info\nvectome version 0.0.1:\n group-0: {'landmarks': 113, 'manifest file': '.../vectome/vectome/data/landmarks/group-0/manifest.json', 'built': True}\n group-1: {'landmarks': 4, 'manifest file': '.../vectome/vectome/data/landmarks/group-1/manifest.json', 'built': True}\n group-2: {'landmarks': 1, 'manifest file': '.../vectome/vectome/data/landmarks/group-2/manifest.json', 'built': False}\n meta: {'cache location': '.../vectome/vectome/data/landmarks', 'cache exists': True}\n```\n\n## Issues, problems, suggestions\n\nAdd to the [issue tracker](https://www.github.com/scbirlab/vectome/issues).\n\n## Documentation\n\n(To come at [ReadTheDocs](https://vectome.readthedocs.org).)\n",
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