# GapClean (v1.0.2)
###### Written by Aarya Venkat, PhD
<img src="gapclean.png" width="350">
#### Description:
GapClean takes a gappy multiple sequence alignment and removes columns with gaps at a
specified threshold value to produce a "cleaner" and easier to visualize sequence alignment.
Can also be used to remove gaps in an alignment relative to a seed sequence to assess site-wise mutational
information.
#### Usage: gapclean [options]
`-i` Input file (Required)
`-o` Output file (Required)
`-t` Threshold value (Optional) Cannot be used with seed argument
`-s` Seed index (Optional) Cannot be used with threshold argument
`-h` Display this help message
##### Example: `gapclean -i input.fa -o output.fa -t 75`
Removes column from alignment when >75 percent of the column are gaps
##### Example: `gapclean -i input.fa -o output.fa -s 0`
Takes first sequence as the seed and removes gaps relative to seed.
## INSTALLATION:
1. `pip install gapclean`
2. Thank Gappy for his service. He is a retired detective.
Raw data
{
"_id": null,
"home_page": null,
"name": "gapclean",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": null,
"keywords": "sequence alignment, bioinformatics, computational biology, protein",
"author": "Aarya Venkat, PhD",
"author_email": null,
"download_url": "https://files.pythonhosted.org/packages/63/97/c4099317d2019a54758606b9b836558014fedcdd364d13883a855e4fa0c2/gapclean-1.0.2.tar.gz",
"platform": null,
"description": "# GapClean (v1.0.2) \n###### Written by Aarya Venkat, PhD\n<img src=\"gapclean.png\" width=\"350\">\n\n#### Description: \nGapClean takes a gappy multiple sequence alignment and removes columns with gaps at a \nspecified threshold value to produce a \"cleaner\" and easier to visualize sequence alignment.\n\nCan also be used to remove gaps in an alignment relative to a seed sequence to assess site-wise mutational\ninformation. \n\n#### Usage: gapclean [options]\n\n `-i` Input file (Required)\n\n `-o` Output file (Required)\n\n `-t` Threshold value (Optional) Cannot be used with seed argument\n\n `-s` Seed index (Optional) Cannot be used with threshold argument\n\n `-h` Display this help message\n\n\n##### Example: `gapclean -i input.fa -o output.fa -t 75` \nRemoves column from alignment when >75 percent of the column are gaps \n\n##### Example: `gapclean -i input.fa -o output.fa -s 0` \nTakes first sequence as the seed and removes gaps relative to seed.\n\n \n \n## INSTALLATION:\n\n1. `pip install gapclean`\n\n2. Thank Gappy for his service. He is a retired detective.\n",
"bugtrack_url": null,
"license": null,
"summary": "Clean up large gappy multiple sequence alignments.",
"version": "1.0.2",
"project_urls": {
"Github": "https://github.com/arikat/GapClean",
"Homepage": "https://aaryakat.com"
},
"split_keywords": [
"sequence alignment",
" bioinformatics",
" computational biology",
" protein"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "b30077cf1c2ce5e8de2b80a1d063223171a00bf60aa8ad2896c7e09dc4b13947",
"md5": "acf2b0776529d6c10f59982ff704724b",
"sha256": "955bd5daacd743ca004df273e9d1c2c00d4056b6aef5cf476383ebed6150a71d"
},
"downloads": -1,
"filename": "gapclean-1.0.2-py3-none-any.whl",
"has_sig": false,
"md5_digest": "acf2b0776529d6c10f59982ff704724b",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 6146,
"upload_time": "2025-01-06T23:12:30",
"upload_time_iso_8601": "2025-01-06T23:12:30.463369Z",
"url": "https://files.pythonhosted.org/packages/b3/00/77cf1c2ce5e8de2b80a1d063223171a00bf60aa8ad2896c7e09dc4b13947/gapclean-1.0.2-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "6397c4099317d2019a54758606b9b836558014fedcdd364d13883a855e4fa0c2",
"md5": "9cf16db59e82a76cd44277ee4ee3c1f0",
"sha256": "91e81b2ae2530345a171cbd51d2588c6c8827360cd91214c9a8734b3e227e3dd"
},
"downloads": -1,
"filename": "gapclean-1.0.2.tar.gz",
"has_sig": false,
"md5_digest": "9cf16db59e82a76cd44277ee4ee3c1f0",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 5659,
"upload_time": "2025-01-06T23:12:32",
"upload_time_iso_8601": "2025-01-06T23:12:32.363437Z",
"url": "https://files.pythonhosted.org/packages/63/97/c4099317d2019a54758606b9b836558014fedcdd364d13883a855e4fa0c2/gapclean-1.0.2.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2025-01-06 23:12:32",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "arikat",
"github_project": "GapClean",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"lcname": "gapclean"
}