| Name | PhyloFunc JSON |
| Version |
1.0.7
JSON |
| download |
| home_page | None |
| Summary | Generate PhyloFunc to incorporate microbiome phylogeny to inform on metaproteomic functional distance. |
| upload_time | 2024-12-03 16:35:09 |
| maintainer | None |
| docs_url | None |
| author | Luman Wang |
| requires_python | None |
| license | None |
| keywords |
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# PhyloFunc
'PhyloFunc' is a Python package for generating PhyloFunc to incorporate microbiome phylogeny to inform on metaproteomic functional distance.
It enables efficient calculation of functional beta-diversity distances between sample pairs and generates comprehensive distance metrics across multiple samples.
## Installation of package
You can install this package via pip:
pip install PhyloFunc
## Usage
Once installed, you can use the PhyloFunc package in a Python script or an interactive environment.
### Quick Start
#### Import package
from PhyloFunc import PhyloFunc_distance
from PhyloFunc import PhyloFunc_matrix
#### Script
Two input parameters are required. The first is a phylogenetic tree (default: bac120_iqtree_v2.0.1.nwk). The second is a phylogeny-informed Taxon-Function table, which includes columns labeled Taxon, Function, and the names of samples (default: Taxon_Function_distance.csvor Taxon_Function_matrix.csv).
#### 1. Calculate PhyloFunc distance between sample pairs
PhyloFunc_distance(tree_file='bac120_iqtree_v2.0.1.nwk', sample_file='Taxon_Function_distance.csv')
#### 2. Calculate PhyloFunc distance matrix across multiple samples
PhyloFunc_matrix(tree_file='bac120_iqtree_v2.0.1.nwk', sample_file='Taxon_Function_matrix.csv')
### Output
PhyloFunc distance or PhyloFunc distance matrix can be output.
## Performance optimization
This package improves performance by reducing disk I/O operations and processing data in memory. This enables faster computations with large datasets.
## Project structure
```
PhyloFunc/
├── __init__.py
├── PhyloFunc.py
│ └── The main function code.
├── data/
│ ├── Taxon_Function_distance.csv
│ │ └── Data file for calculating the distance between two samples.
│ ├── Taxon_Function_matrix.csv
│ │ └── Data file for calculating distances matrix across multiple samples.
│ └── bac120_iqtree_v2.0.1.nwk
│ └── Phylogenetic tree file.
└── PhyloFunc_Package_Tutorial.ipynb
└── Demonstrates the specific application of this package.
```
## Contribution
Welcome code contributions and improvement suggestions! Feel free to submit an issue or a pull request on GitHub.
## License
This project uses an MIT license. For details, see the LICENSE file.
## Application
For more detailed usage instructions, please refer to the paper：
Wang and Li et al., PhyloFunc: Phylogeny-informed Functional Distance as a New Ecological Metric for Metaproteomic Data Analysis
doi: https://doi.org/10.1101/2024.05.28.596184
Raw data
{
"_id": null,
"home_page": null,
"name": "PhyloFunc",
"maintainer": null,
"docs_url": null,
"requires_python": null,
"maintainer_email": null,
"keywords": null,
"author": "Luman Wang",
"author_email": "lumanottawa@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/0c/5b/a4c9a4484ded9b977c53c01ccda18ed4721df4760d51779a69791f83f120/PhyloFunc-1.0.7.tar.gz",
"platform": null,
"description": "# PhyloFunc\r\n\r\n'PhyloFunc' is a Python package for generating PhyloFunc to incorporate microbiome phylogeny to inform on metaproteomic functional distance. \r\nIt enables efficient calculation of functional beta-diversity distances between sample pairs and generates comprehensive distance metrics across multiple samples.\r\n\r\n## Installation of package\r\n\r\nYou can install this package via pip: \r\npip install PhyloFunc\r\n\r\n## Usage\r\nOnce installed, you can use the PhyloFunc package in a Python script or an interactive environment.\r\n\r\n### Quick Start\r\n\r\n#### Import package\r\n\r\nfrom PhyloFunc import PhyloFunc_distance \r\nfrom PhyloFunc import PhyloFunc_matrix\r\n\r\n#### Script\r\nTwo input parameters are required. The first is a phylogenetic tree (default: bac120_iqtree_v2.0.1.nwk). The second is a phylogeny-informed Taxon-Function table, which includes columns labeled Taxon, Function, and the names of samples (default: Taxon_Function_distance.csvor Taxon_Function_matrix.csv).\r\n\r\n#### 1. Calculate PhyloFunc distance between sample pairs\r\nPhyloFunc_distance(tree_file='bac120_iqtree_v2.0.1.nwk', sample_file='Taxon_Function_distance.csv')\r\n\r\n#### 2. Calculate PhyloFunc distance matrix across multiple samples\r\nPhyloFunc_matrix(tree_file='bac120_iqtree_v2.0.1.nwk', sample_file='Taxon_Function_matrix.csv')\r\n\r\n### Output\r\nPhyloFunc distance or PhyloFunc distance matrix can be output.\r\n\r\n## Performance optimization\r\nThis package improves performance by reducing disk I/O operations and processing data in memory. This enables faster computations with large datasets.\r\n\r\n## Project structure\r\n```\r\nPhyloFunc/ \r\n\u251c\u2500\u2500 __init__.py \r\n\u251c\u2500\u2500 PhyloFunc.py \r\n\u2502 \u2514\u2500\u2500 The main function code. \r\n\u251c\u2500\u2500 data/ \r\n\u2502 \u251c\u2500\u2500 Taxon_Function_distance.csv\r\n\u2502 \u2502 \u2514\u2500\u2500 Data file for calculating the distance between two samples. \r\n\u2502 \u251c\u2500\u2500 Taxon_Function_matrix.csv\r\n\u2502 \u2502 \u2514\u2500\u2500 Data file for calculating distances matrix across multiple samples. \r\n\u2502 \u2514\u2500\u2500 bac120_iqtree_v2.0.1.nwk \r\n\u2502 \u2514\u2500\u2500 Phylogenetic tree file. \r\n\u2514\u2500\u2500 PhyloFunc_Package_Tutorial.ipynb\r\n \u2514\u2500\u2500 Demonstrates the specific application of this package.\r\n```\r\n\r\n## Contribution\r\nWelcome code contributions and improvement suggestions! Feel free to submit an issue or a pull request on GitHub.\r\n\r\n## License\r\nThis project uses an MIT license. For details, see the LICENSE file.\r\n\r\n## Application\r\nFor more detailed usage instructions, please refer to the paper\uff1a\r\nWang and Li et al., PhyloFunc: Phylogeny-informed Functional Distance as a New Ecological Metric for Metaproteomic Data Analysis\r\ndoi: https://doi.org/10.1101/2024.05.28.596184\r\n",
"bugtrack_url": null,
"license": null,
"summary": "Generate PhyloFunc to incorporate microbiome phylogeny to inform on metaproteomic functional distance.",
"version": "1.0.7",
"project_urls": null,
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "f4dda80eb558d143b5698cc129fcc2dbcb79d46ba873b693f61905ed056858c6",
"md5": "c79a44b77ee8277216379b3bc3e50e0f",
"sha256": "924974ce6f2bee97aeb42bcf205a3a875c123822061236bdf973076e75faf99e"
},
"downloads": -1,
"filename": "PhyloFunc-1.0.7-py3-none-any.whl",
"has_sig": false,
"md5_digest": "c79a44b77ee8277216379b3bc3e50e0f",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 1317551,
"upload_time": "2024-12-03T16:35:06",
"upload_time_iso_8601": "2024-12-03T16:35:06.572224Z",
"url": "https://files.pythonhosted.org/packages/f4/dd/a80eb558d143b5698cc129fcc2dbcb79d46ba873b693f61905ed056858c6/PhyloFunc-1.0.7-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "0c5ba4c9a4484ded9b977c53c01ccda18ed4721df4760d51779a69791f83f120",
"md5": "022c7f438d9e79a4daf53c6254fb9492",
"sha256": "f3b836455ebdef1f4a1a2509e5d4c2250804c0ca88bce3a571e24c760ce18e23"
},
"downloads": -1,
"filename": "PhyloFunc-1.0.7.tar.gz",
"has_sig": false,
"md5_digest": "022c7f438d9e79a4daf53c6254fb9492",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 1309937,
"upload_time": "2024-12-03T16:35:09",
"upload_time_iso_8601": "2024-12-03T16:35:09.158520Z",
"url": "https://files.pythonhosted.org/packages/0c/5b/a4c9a4484ded9b977c53c01ccda18ed4721df4760d51779a69791f83f120/PhyloFunc-1.0.7.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-12-03 16:35:09",
"github": false,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"lcname": "phylofunc"
}
