Metadata-Version: 2.1
Name: ngsfragments
Version: 2.4.4
Summary: Python package for Next Generation Sequencing fragment manipulation
Home-page: https://github.com/kylessmith/ngsfragments
License: GPL-2.0-or-later
Keywords: cython,interval,ngsfragments,c
Author: Kyle S. Smith
Author-email: kyle.smith@stjude.org
Maintainer: Kyle S. Smith
Maintainer-email: kyle.smith@stjude.org
Requires-Python: >=3.10
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Dist: ailist (>=2.1.3,<3.0.0)
Requires-Dist: bokeh (>=3.1.0,<4.0.0)
Requires-Dist: cython (>=3.0.0,<4.0.0)
Requires-Dist: genome_info (>=1.0.6,<2.0.0)
Requires-Dist: h5py (>=3.8.0,<4.0.0)
Requires-Dist: hmmCNV (>=1.1.6,<2.0.0)
Requires-Dist: intervalframe (>=1.1.7,<2.0.0)
Requires-Dist: linear_segment (>=1.2.1,<2.0.0)
Requires-Dist: loess (>=2.1.2)
Requires-Dist: matplotlib (>=3.7.1,<4.0.0)
Requires-Dist: numpy (>=1.23.5)
Requires-Dist: pandas (>=2.0.0,<3.0.0)
Requires-Dist: projectframe (>=1.0.4,<2.0.0)
Requires-Dist: pysam (>=0.21.0)
Requires-Dist: scikit-learn (>=1.2.2,<2.0.0)
Requires-Dist: scipy (>=1.9.1)
Requires-Dist: seaborn (>=0.12.2)
Requires-Dist: statsmodels (>=0.13.5)
Project-URL: Documentation, https://www.biosciencestack.com/static/ngsfragments/docs/index.html
Project-URL: Repository, https://github.com/kylessmith/ngsfragments
Description-Content-Type: text/markdown

# Next Generation Sequencing fragment manipulation

[![Build Status](https://travis-ci.org/kylessmith/NGSfragments.svg?branch=master)](https://travis-ci.org/kylessmith/NGSfragments) [![PyPI version](https://badge.fury.io/py/NGSfragments.svg)](https://badge.fury.io/py/NGSfragments)

This is a Python package for easy and efficient manipulation
of Next Generation Sequencing reads.


## Install

If you dont already have numpy and scipy installed, it is best to download
`Anaconda`, a python distribution that has them included.  
```
    https://continuum.io/downloads
```

Dependencies can be installed by:

```
    pip install -r requirements.txt
```

PyPI install, presuming you have all its requirements installed:
```
    pip install NGSfragments
```

## Usage

```python
from NGSfragments import fragments
import numpy as np

# Create data
frags = fragments("test_bam.bam", verbose=True)
```

