Metadata-Version: 2.1
Name: nanoepiseg
Version: 1.0.0b3
Summary: Methylome segmentation algorithm using a changepoint detection HMM
Home-page: https://github.com/snajder-r/nanoepiseg
Author: Rene Snajder
Author-email: r.snajder@dkfz-heidelberg.de
License: MIT
Description: # NanoEpiSeg 1.0.0b3
        
        [![GitHub license](https://img.shields.io/github/license/snajder-r/nanoepiseg)](https://github.com/snajder-r/nanoepiseg/blob/master/LICENSE)
        [![Language](https://img.shields.io/badge/Language-Python3.7+-yellow.svg)](https://www.python.org/)
        [![Build Status](https://travis-ci.com/snajder-r/nanoepiseg.svg?branch=main)](https://travis-ci.com/snajder-r/nanoepiseg)
        [![Code style: black](https://img.shields.io/badge/code%20style-black-black.svg?style=flat)](https://github.com/snajder-r/black "Black (modified)")
        
        [![PyPI version](https://badge.fury.io/py/nanoepiseg.svg)](https://badge.fury.io/py/nanoepiseg)
        [![PyPI downloads](https://pepy.tech/badge/nanoepiseg)](https://pepy.tech/project/nanoepiseg)
        [![Anaconda Version](https://img.shields.io/conda/v/snajder-r/nanoepiseg?color=blue)](https://anaconda.org/snajder-r/nanoepiseg)
        [![Anaconda Downloads](https://anaconda.org/snajder-r/nanoepiseg/badges/downloads.svg)](https://anaconda.org/snajder-r/nanoepiseg)
        
        NanoEpiSeg is a tool for *de novo* segmentation of  a methylome from read-level methylation calls (such as Nanopolish).
        
        NanoEpiSeg is currently in development. Please do not hesitate to report bugs or feature requests.
        
        A detailed documentation is in the works, stay tuned!
        ## Prerequisites
        
        NanoEpiSeg assumes that your methylation calls are stored in [MetH5](http://github.com/snajder-r/meth5format) format.
        
        ## Installation
        
        Through pip:
        
        ```
        pip install nanoepiseg
        ````
        
        Through anaconda:
        
        ```
        conda install -c snajder-r nanoepiseg
        ```
        
        ## Usage
        
        NanoEpiSeg is meant to be parallelizable, which is why you would typically call nanoepiseg on a cluster system in parallel.
        In order to best accomplish load-balancing, it is done per hdf5 chunk. 
        
        You can list the number of chunks per chromosome via:
        
        ```bash
        nanoepiseg list_chunks --m5file INPUT_FILE.m5
        ```
        
        To then perform segmentation for a certain chunk, you can run:
        
        ```bash
        nanoepiseg segment_h5 --m5file INPUT_FILE.m5 \
            --out_tsv OUTPUT_FILE \ 
            --reader_workers NUM_READER_WORKERS \ 
            --workers NUM_SEGMENTATION_WORKERS \ 
            --chromosome CHROMOSOME \
            --chunks CHUNK1 [CHUNK2 ...]
        ```
        
        There are further options available. Please check out the help to discover them.
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Description-Content-Type: text/markdown
