==========
fibertools
==========
.. image:: https://img.shields.io/pypi/v/fibertools.svg
:target: https://pypi.python.org/pypi/fibertools
.. image:: https://img.shields.io/travis/mrvollger/fibertools.svg
:target: https://travis-ci.com/mrvollger/fibertools
.. image:: https://readthedocs.org/projects/fibertools/badge/?version=latest
:target: https://fibertools.readthedocs.io/en/latest/?version=latest
:alt: Documentation Status
.. image:: https://pyup.io/repos/github/mrvollger/fibertools/shield.svg
:target: https://pyup.io/repos/github/mrvollger/fibertools/
:alt: Updates
A python package for handling Fiber-seq data.
* Free software: MIT license
* Documentation: https://fibertools.readthedocs.io.
Install
-------
::
pip install fibertools
Features
--------
::
usage: fibertools [-h] [-t THREADS] [-v] [-V] {bam2bed,add-m6a,add-nucleosomes,model,split,trackhub,bed2d4} ...
positional arguments:
{bam2bed,add-m6a,add-nucleosomes,model,split,trackhub,bed2d4}
Available subcommand for fibertools
bam2bed Extract m6a calls from bam and output bed12.
add-m6a Add m6A tag
add-nucleosomes Add Nucleosome and MSP tags
model Make MSP features
split Split a bed over many output files.
trackhub Make a trackhub from a bed file.
bed2d4 Make a multi-track d4 file from a bed file.
optional arguments:
-h, --help show this help message and exit
-t THREADS, --threads THREADS
n threads to use (default: 1)
-v, --verbose increase logging verbosity (default: False)
-V, --version show program's version number and exit
Add nucleosomes and MSPs to a fibertools-rs m6A bam
---------------------------------------------------
Create the model ::
fibertools add-nucleosomes --input input.bam > model.json
Add nucleosomes with the model::
fibertools add-nucleosomes --input input.bam --model model.json > output.bam
Note that by default the input bam file is read from stdin and the output bam file is written to stdout.
Credits
-------
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
=======
History
=======
0.1.0 (2022-05-01)
------------------
* First release on PyPI.
Raw data
{
"_id": null,
"home_page": "https://github.com/mrvollger/fibertools",
"name": "fibertools",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.6",
"maintainer_email": "",
"keywords": "fibertools",
"author": "Mitchell R. Vollger",
"author_email": "mrvollger@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/78/b4/06c7c526b7405e768e04eea3d688d4a0f25ba6fbb2fd085d5a9221b0f9ed/fibertools-0.3.0.tar.gz",
"platform": null,
"description": "==========\nfibertools\n==========\n\n\n.. image:: https://img.shields.io/pypi/v/fibertools.svg\n :target: https://pypi.python.org/pypi/fibertools\n\n.. image:: https://img.shields.io/travis/mrvollger/fibertools.svg\n :target: https://travis-ci.com/mrvollger/fibertools\n\n.. image:: https://readthedocs.org/projects/fibertools/badge/?version=latest\n :target: https://fibertools.readthedocs.io/en/latest/?version=latest\n :alt: Documentation Status\n\n\n.. image:: https://pyup.io/repos/github/mrvollger/fibertools/shield.svg\n :target: https://pyup.io/repos/github/mrvollger/fibertools/\n :alt: Updates\n\n\n\nA python package for handling Fiber-seq data.\n\n\n* Free software: MIT license\n* Documentation: https://fibertools.readthedocs.io.\n\nInstall\n-------\n\n::\n\n pip install fibertools\n\nFeatures\n--------\n\n::\n\n usage: fibertools [-h] [-t THREADS] [-v] [-V] {bam2bed,add-m6a,add-nucleosomes,model,split,trackhub,bed2d4} ...\n\n positional arguments:\n {bam2bed,add-m6a,add-nucleosomes,model,split,trackhub,bed2d4}\n Available subcommand for fibertools\n bam2bed Extract m6a calls from bam and output bed12.\n add-m6a Add m6A tag\n add-nucleosomes Add Nucleosome and MSP tags\n model Make MSP features\n split Split a bed over many output files.\n trackhub Make a trackhub from a bed file.\n bed2d4 Make a multi-track d4 file from a bed file.\n\n optional arguments:\n -h, --help show this help message and exit\n -t THREADS, --threads THREADS\n n threads to use (default: 1)\n -v, --verbose increase logging verbosity (default: False)\n -V, --version show program's version number and exit\n\n\nAdd nucleosomes and MSPs to a fibertools-rs m6A bam\n---------------------------------------------------\n\nCreate the model ::\n\n fibertools add-nucleosomes --input input.bam > model.json\n\nAdd nucleosomes with the model::\n\n fibertools add-nucleosomes --input input.bam --model model.json > output.bam\n\nNote that by default the input bam file is read from stdin and the output bam file is written to stdout.\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n\n\n=======\nHistory\n=======\n\n0.1.0 (2022-05-01)\n------------------\n\n* First release on PyPI.\n",
"bugtrack_url": null,
"license": "MIT license",
"summary": "A project for handling fiber-seq data.",
"version": "0.3.0",
"project_urls": {
"Homepage": "https://github.com/mrvollger/fibertools"
},
"split_keywords": [
"fibertools"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "bd0d13adc57afde1991c1f0420a20c2739839a1a74fb81aa249dee240131d90f",
"md5": "378dbbf42ed2cee55ef0e8e071a407c0",
"sha256": "6d5bf9fc3affb8efb3d3da26ae518e6df136a3a195edbeb4f90977b7a8ebd0fa"
},
"downloads": -1,
"filename": "fibertools-0.3.0-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "378dbbf42ed2cee55ef0e8e071a407c0",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": ">=3.6",
"size": 28365,
"upload_time": "2023-05-16T18:15:51",
"upload_time_iso_8601": "2023-05-16T18:15:51.622654Z",
"url": "https://files.pythonhosted.org/packages/bd/0d/13adc57afde1991c1f0420a20c2739839a1a74fb81aa249dee240131d90f/fibertools-0.3.0-py2.py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "78b406c7c526b7405e768e04eea3d688d4a0f25ba6fbb2fd085d5a9221b0f9ed",
"md5": "f7d81c2375d34f47c119652f8e6c58f7",
"sha256": "00f07585dd8c67171419acd1725b4a3ff8e1dff505e7a13971405239d76967bd"
},
"downloads": -1,
"filename": "fibertools-0.3.0.tar.gz",
"has_sig": false,
"md5_digest": "f7d81c2375d34f47c119652f8e6c58f7",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.6",
"size": 1209577,
"upload_time": "2023-05-16T18:15:54",
"upload_time_iso_8601": "2023-05-16T18:15:54.089579Z",
"url": "https://files.pythonhosted.org/packages/78/b4/06c7c526b7405e768e04eea3d688d4a0f25ba6fbb2fd085d5a9221b0f9ed/fibertools-0.3.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-05-16 18:15:54",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "mrvollger",
"github_project": "fibertools",
"travis_ci": true,
"coveralls": false,
"github_actions": false,
"requirements": [
{
"name": "sphinx",
"specs": [
[
"==",
"4.2.0"
]
]
},
{
"name": "docutils",
"specs": [
[
"==",
"0.17"
]
]
},
{
"name": "sphinx_rtd_theme",
"specs": []
},
{
"name": "readthedocs-sphinx-search",
"specs": []
},
{
"name": "rstcheck",
"specs": [
[
"==",
"5.0.0"
]
]
},
{
"name": "numba",
"specs": [
[
">=",
"0.53"
]
]
},
{
"name": "polars",
"specs": [
[
">=",
"0.13"
]
]
},
{
"name": "pandas",
"specs": [
[
">=",
"1.4"
]
]
},
{
"name": "numpy",
"specs": [
[
"==",
"1.22"
]
]
},
{
"name": "pysam",
"specs": [
[
"==",
"0.19.0"
]
]
},
{
"name": "pyranges",
"specs": [
[
"==",
"0.0.115"
]
]
},
{
"name": "mokapot",
"specs": [
[
"==",
"0.8"
]
]
},
{
"name": "scikit-learn",
"specs": []
},
{
"name": "xgboost",
"specs": [
[
"==",
"1.5"
]
]
},
{
"name": "Cython",
"specs": []
}
],
"tox": true,
"lcname": "fibertools"
}
JSON
