Metadata-Version: 2.4
Name: ngsfragments
Version: 2.6.2
Summary: Python package for Next Generation Sequencing fragment manipulation
Author-email: "Kyle S. Smith" <kyle.smith@stjude.org>
Maintainer-email: "Kyle S. Smith" <kyle.smith@stjude.org>
License-Expression: GPL-2.0-or-later
Project-URL: Homepage, https://github.com/kylessmith/ngsfragments
Project-URL: Repository, https://github.com/kylessmith/ngsfragments
Project-URL: Documentation, https://www.biosciencestack.com/static/ngsfragments/docs/index.html
Project-URL: Issues, https://github.com/kylessmith/ngsfragments/issues
Keywords: cython,interval,ngsfragments,c
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS
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 :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: numpy>=2.0.0
Requires-Dist: pandas>=2.0.0
Requires-Dist: scipy>=1.9.1
Requires-Dist: ailist<3,>=2.2.1
Requires-Dist: genome_info<2,>=1.1.4
Requires-Dist: pysam<0.24,>=0.23.1
Requires-Dist: intervalframe>=1.2.2
Requires-Dist: linear_segment>=1.2.3
Requires-Dist: projectframe>=1.0.7
Requires-Dist: hmmCNV>=1.1.8
Requires-Dist: loess>=2.1.2
Requires-Dist: scikit-learn>=1.2.2
Requires-Dist: statsmodels>=0.14.0
Requires-Dist: matplotlib>=3.7.1
Requires-Dist: seaborn>=0.12.2
Requires-Dist: bokeh>=3.1.0
Requires-Dist: h5py<4,>=3.8.0
Requires-Dist: pyarrow>=21.0.0
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Requires-Dist: cython-lint; extra == "dev"
Dynamic: license-file

# 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)
```
