Metadata-Version: 2.1
Name: cfdna
Version: 2.0.4
Summary: Python package for fragment manipulation for cfDNA
Home-page: https://github.com/kylessmith/cfdna
License: GPL-2.0-or-later
Keywords: cython,interval,cfdna,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,<4.0
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 (>=2.1.0,<3.0.0)
Requires-Dist: bokeh (>=3.1.0,<4.0.0)
Requires-Dist: cython (>=0.29.32,<0.30.0)
Requires-Dist: hmmCNV (>=1.0.1,<2.0.0)
Requires-Dist: intervalframe (>=1.1.3,<2.0.0)
Requires-Dist: linear_segment (>=1.1.0,<2.0.0)
Requires-Dist: matplotlib (>=3.7.1,<4.0.0)
Requires-Dist: ngsfragments (>=2.0.7,<3.0.0)
Requires-Dist: numpy (>=1.23.5,<2.0.0)
Requires-Dist: pandas (>=1.5.2,<2.0.0)
Requires-Dist: projectframe (>=1.0.0,<2.0.0)
Requires-Dist: pysam (>=0.21.0,<0.22.0)
Requires-Dist: scikit-learn (>=1.2.2,<2.0.0)
Requires-Dist: scipy (>=1.9.1,<2.0.0)
Requires-Dist: seaborn (>=0.12.2,<0.13.0)
Requires-Dist: statsmodels (>=0.13.5,<0.14.0)
Project-URL: Documentation, https://www.biosciencestack.com/static/cfdna/docs/index.html
Project-URL: Repository, https://github.com/kylessmith/cfdna
Description-Content-Type: text/markdown

# Cell-free DNA analysis toolkit

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

This is a Python package for easy and efficient cell-free
DNA analysis.

All citations should reference to [original paper][paper].


## 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 cfdna
```

## Usage

```python
import cfdna as cf
import numpy as np

# Create data
cfdata = cf.cfDNA()
frags = cf.io.readBAM("test.bam")

# Call CNVs
cf.proc.call_cnv_pipline(cfdata, frags)

# Plot CNVs
cf.pl.plot_cnv(cfdata, "test.bam")
```

Run from the commadline:

```
    python -m cfdna callCNVs --bam test.bam --segs
```

This will output a .png plot and seg file.

[paper]: https://www.cell.com/cancer-cell/pdfExtended/S1535-6108(21)00501-8
