| Name | hardyweinbergcalculator JSON |
| Version |
0.3.6
JSON |
| download |
| home_page | https://github.com/dellius-alexander/Hardy-Weinberg.git |
| Summary | Hardy-Weinberg Equilibrium Calculator. Calculates the expected genotype frequencies based on the allele frequencies of a population in Hardy-Weinberg equilibrium. |
| upload_time | 2023-06-25 23:42:54 |
| maintainer | info@hyfisolutions.com |
| docs_url | None |
| author | Dellius Alexander |
| requires_python | >=3.7 |
| license | MIT License Copyright (c) 2023 Dellius Alexander 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 copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 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 |
hardy-weinberg-equilibrium
hardy-weinberg-equilibrium-calculator
hardy-weinberg-calculator
chi-square
chi-square-test
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[](https://github.com/dellius-alexander/Hardy-Weinberg/actions/workflows/deploy.yml)
---
# Hardy Weinberg Equilibrium
Hardy-Weinberg Equilibrium Calculator. Calculates the expected
genotype frequencies based on the allele frequencies of a
population in Hardy-Weinberg equilibrium.
## Installation
```bash
pip install hardyweinbergcalculator
```
## Usage
```text
usage: hwc [-h] [--version] [--verbose] [--debug] [--samples SAMPLES] [--p P] [--q Q] [--tpop TPOP] [--ppop PPOP] [--qpop QPOP] [--pq2pop PQ2POP] [--genes GENES [GENES ...]] [--json JSON [JSON ...]]
Hardy-Weinberg Equilibrium Calculator. Calculates the expected genotype frequencies based on the allele frequencies of a population in Hardy-Weinberg equilibrium. See: https://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--verbose Enable verbose logging. (default: False)
--debug Enable debug logging. (default: False)
--samples SAMPLES Number of samples to generate, if using random data generator. (default: None)
--p P Frequency of dominant allele. (default: None)
--q Q Frequency of recessive allele. (default: None)
--tpop TPOP Total population. (default: None)
--ppop PPOP Original population of dominant allele. (default: None)
--qpop QPOP Original population of recessive allele. (default: None)
--pq2pop PQ2POP Original population of heterozygous allele. (default: None)
Example: python3 -m hwc --ppop 10 --qpop 10 --pq2pop 200 --verbose
```
### Generate random data
```bash
python3 -m hwc --samples 1000 --verbose
```
### Calculate from known data
```bash
python3 -m hwc --ppop 10 --qpop 10 --pq2pop 200 --verbose
```
## In your code
### Test for Hard-Weinberg Equilibrium from generated data
```python
from hwc import generate_population, HardyWeinberg
# Generate random data
population = generate_population(n=1000)
res = HardyWeinberg(genes=population)
print(res)
```
### Test for Hardy-Weinberg Equilibrium from known data
```python
from hwc import HardyWeinberg
# Known data
res = HardyWeinberg(
homozygous_dominant_population=20,
homozygous_recessive_population=44,
heterozygous_population=95
)
print(res)
```
### Results Data Object
The results returned from the Hardyweinberg test will ultimately look like this, in json format:
```json
{
"2*pq": 0.4986501057404244,
"chi_square_test": 20.439848879167698,
"expected_heterozygous_population": 1132.434390136504,
"expected_homozygous_dominant_population": 510.28280493174816,
"expected_homozygous_recessive_population": 628.2828049317482,
"genes": [],
"heterozygous_population": 1025.0,
"homozygous_dominant_population": 564.0,
"homozygous_recessive_population": 682.0,
"p": 0.47402025539409953,
"p + q": 1.0,
"p**2": 0.22469520252388733,
"p**2 + 2*pq + q**2": 1.0,
"q": 0.5259797446059005,
"q**2": 0.2766546917356883,
"total_population": 2271.0
}
```
Raw data
{
"_id": null,
"home_page": "https://github.com/dellius-alexander/Hardy-Weinberg.git",
"name": "hardyweinbergcalculator",
"maintainer": "info@hyfisolutions.com",
"docs_url": null,
"requires_python": ">=3.7",
"maintainer_email": "info@hyfisolutions.com",
"keywords": "hardy-weinberg-equilibrium,hardy-weinberg-equilibrium-calculator,hardy-weinberg-calculator,chi-square,chi-square-test",
"author": "Dellius Alexander",
"author_email": "info@hyfisolutions.com",
"download_url": "https://files.pythonhosted.org/packages/3e/07/7b6bf2056a2ddb5302fcdebd862bd82ec827d0e34d1655410383037077e4/hardyweinbergcalculator-0.3.6.zip",
"platform": null,
"description": "[](https://github.com/dellius-alexander/Hardy-Weinberg/actions/workflows/deploy.yml)\n\n---\n\n# Hardy Weinberg Equilibrium\n\n\nHardy-Weinberg Equilibrium Calculator. Calculates the expected \ngenotype frequencies based on the allele frequencies of a \npopulation in Hardy-Weinberg equilibrium.\n\n## Installation\n\n```bash\npip install hardyweinbergcalculator\n```\n\n## Usage\n\n```text\nusage: hwc [-h] [--version] [--verbose] [--debug] [--samples SAMPLES] [--p P] [--q Q] [--tpop TPOP] [--ppop PPOP] [--qpop QPOP] [--pq2pop PQ2POP] [--genes GENES [GENES ...]] [--json JSON [JSON ...]]\n\nHardy-Weinberg Equilibrium Calculator. Calculates the expected genotype frequencies based on the allele frequencies of a population in Hardy-Weinberg equilibrium. See: https://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle\n\n\noptional arguments:\n -h, --help show this help message and exit\n --version show program's version number and exit\n --verbose Enable verbose logging. (default: False)\n --debug Enable debug logging. (default: False)\n --samples SAMPLES Number of samples to generate, if using random data generator. (default: None)\n --p P Frequency of dominant allele. (default: None)\n --q Q Frequency of recessive allele. (default: None)\n --tpop TPOP Total population. (default: None)\n --ppop PPOP Original population of dominant allele. (default: None)\n --qpop QPOP Original population of recessive allele. (default: None)\n --pq2pop PQ2POP Original population of heterozygous allele. (default: None)\n\nExample: python3 -m hwc --ppop 10 --qpop 10 --pq2pop 200 --verbose\n```\n\n### Generate random data\n\n```bash \npython3 -m hwc --samples 1000 --verbose\n```\n\n### Calculate from known data\n\n```bash\npython3 -m hwc --ppop 10 --qpop 10 --pq2pop 200 --verbose\n```\n\n## In your code\n\n### Test for Hard-Weinberg Equilibrium from generated data\n\n```python\nfrom hwc import generate_population, HardyWeinberg\n\n# Generate random data\npopulation = generate_population(n=1000)\nres = HardyWeinberg(genes=population)\nprint(res)\n```\n\n### Test for Hardy-Weinberg Equilibrium from known data\n\n```python\nfrom hwc import HardyWeinberg\n\n# Known data\nres = HardyWeinberg(\n homozygous_dominant_population=20,\n homozygous_recessive_population=44,\n heterozygous_population=95\n )\nprint(res)\n```\n\n### Results Data Object\n\nThe results returned from the Hardyweinberg test will ultimately look like this, in json format:\n\n```json\n{\n \"2*pq\": 0.4986501057404244,\n \"chi_square_test\": 20.439848879167698,\n \"expected_heterozygous_population\": 1132.434390136504,\n \"expected_homozygous_dominant_population\": 510.28280493174816,\n \"expected_homozygous_recessive_population\": 628.2828049317482,\n \"genes\": [],\n \"heterozygous_population\": 1025.0,\n \"homozygous_dominant_population\": 564.0,\n \"homozygous_recessive_population\": 682.0,\n \"p\": 0.47402025539409953,\n \"p + q\": 1.0,\n \"p**2\": 0.22469520252388733,\n \"p**2 + 2*pq + q**2\": 1.0,\n \"q\": 0.5259797446059005,\n \"q**2\": 0.2766546917356883,\n \"total_population\": 2271.0\n}\n\n```\n\n\n",
"bugtrack_url": null,
"license": "MIT License Copyright (c) 2023 Dellius Alexander 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 copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 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. ",
"summary": "Hardy-Weinberg Equilibrium Calculator. Calculates the expected genotype frequencies based on the allele frequencies of a population in Hardy-Weinberg equilibrium.",
"version": "0.3.6",
"project_urls": {
"Homepage": "https://github.com/dellius-alexander/Hardy-Weinberg.git"
},
"split_keywords": [
"hardy-weinberg-equilibrium",
"hardy-weinberg-equilibrium-calculator",
"hardy-weinberg-calculator",
"chi-square",
"chi-square-test"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "732bb22edaff197484dabb05c69f10bba76d89b5962bfb70a20373ce987b922c",
"md5": "bcfcdd234f9395e63e59651faf7a156c",
"sha256": "242f1130b2871a239766d270c5252a10368d27b4f4ab7a78b3b3914f48945ff2"
},
"downloads": -1,
"filename": "hardyweinbergcalculator-0.3.6-py3-none-any.whl",
"has_sig": false,
"md5_digest": "bcfcdd234f9395e63e59651faf7a156c",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.7",
"size": 14757,
"upload_time": "2023-06-25T23:42:53",
"upload_time_iso_8601": "2023-06-25T23:42:53.012211Z",
"url": "https://files.pythonhosted.org/packages/73/2b/b22edaff197484dabb05c69f10bba76d89b5962bfb70a20373ce987b922c/hardyweinbergcalculator-0.3.6-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "3e077b6bf2056a2ddb5302fcdebd862bd82ec827d0e34d1655410383037077e4",
"md5": "875c263fef1a980bf5fcad8365112ea7",
"sha256": "b63bc340bb90ba762abda1e06d370771ed4002c6296338ac630edcea2e6ce96c"
},
"downloads": -1,
"filename": "hardyweinbergcalculator-0.3.6.zip",
"has_sig": false,
"md5_digest": "875c263fef1a980bf5fcad8365112ea7",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7",
"size": 22308,
"upload_time": "2023-06-25T23:42:54",
"upload_time_iso_8601": "2023-06-25T23:42:54.125776Z",
"url": "https://files.pythonhosted.org/packages/3e/07/7b6bf2056a2ddb5302fcdebd862bd82ec827d0e34d1655410383037077e4/hardyweinbergcalculator-0.3.6.zip",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-06-25 23:42:54",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "dellius-alexander",
"github_project": "Hardy-Weinberg",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [],
"lcname": "hardyweinbergcalculator"
}
