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Metadata-Version: 1.2
Name: nanomath
Version: 1.2.0
Summary: A few simple math function for other Oxford Nanopore processing scripts
Home-page: https://github.com/wdecoster/nanomath
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: GPLv3
Description: # nanomath
        This module provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data
        
        [![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster)](https://twitter.com/wouter_decoster)
        [![install with conda](https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanomath)
        [![install with Debian](https://www.debian.org/logos/button-mini.png)](https://tracker.debian.org/pkg/python-nanomath)
        [![Build Status](https://travis-ci.org/wdecoster/nanomath.svg?branch=master)](https://travis-ci.org/wdecoster/nanomath)
        [![Code Health](https://landscape.io/github/wdecoster/nanomath/master/landscape.svg?style=flat)](https://landscape.io/github/wdecoster/nanomath/master)
        
        
        ## FUNCTIONS
        * Calculate read N50 from a set of lengths `get_N50(readlenghts)`  
        * Remove extreme length outliers from a dataset `remove_length_outliers(dataframe, columname)`  
        * Calculate the average Phred quality of a read `ave_qual(qualscores)`  
        * Write out the statistics report after calling readstats function `write_stats(dataframe, outputname)`  
        * Compute a number of statistics, return a dictionary `calc_read_stats(dataframe)`  
        
        
        ## INSTALLATION
        ```bash
        pip install nanomath
        ```
        or  
        [![install with conda](https://anaconda.org/bioconda/nanomath/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanomath)
        ```
        conda install -c bioconda nanomath
        ```
        
        ## STATUS 
        [![Build Status](https://travis-ci.org/wdecoster/nanomath.svg?branch=master)](https://travis-ci.org/wdecoster/nanomath)
        
        
        ## CONTRIBUTORS
        [@alexomics](https://github.com/alexomics) for fixing the indentation of the printed stats
        
        
        ## CITATION
        If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
        
Keywords: nanopore sequencing plotting quality control
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Requires-Python: >=3