Metadata-Version: 2.1
Name: methplotlib
Version: 0.8.0
Summary: Plot methylation data obtained from nanopolish
Home-page: https://github.com/wdecoster/methplotlib
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: MIT
Description: [![Build Status](https://travis-ci.com/wdecoster/methplotlib.svg?branch=master)](https://travis-ci.com/wdecoster/methplotlib)
        [![Anaconda-Server Badge](https://anaconda.org/bioconda/methplotlib/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)
        [![Anaconda-Server Badge](https://anaconda.org/bioconda/methplotlib/badges/version.svg)](https://anaconda.org/bioconda/methplotlib)
        [![Anaconda-Server Badge](https://anaconda.org/bioconda/methplotlib/badges/license.svg)](https://anaconda.org/bioconda/methplotlib)
        
        # METHPLOTLIB
        
        This script takes data from nanopolish, either as methylation calls or methylation frequencies (as processed by calculate_methylation_frequency.py) to generate a genome browser view on a window.
        
        ## INSTALLATION
        `pip install methplotlib`
        
        ## USAGE
        ```
        methplotlib [-h] [-v] -m METHYLATION [METHYLATION ...] -n NAMES
                       [NAMES ...] -w WINDOW [-g GTF] [-b BED] [--simplify]
                       [--split] [--smooth SMOOTH]
        
        Arguments:
          -h, --help            show this help message and exit
          -v, --version         Print version and exit.
          -m, --methylation METHYLATION [METHYLATION ...]
                                nanoplish calls or frequency output
          -n, --names NAMES [NAMES ...]
                                names of datasets in --methylation
          -w, --window WINDOW   window (region) to which the visualisation has to be restricted
          -g, --gtf GTF         add annotation based on a gtf file
          -b, --bed BED         add annotation based on a bed file matching to your reference genome
          --simplify            simplify annotation track to show genes rather than transcripts
          --split               split, rather than overlay the methylation frequency tracks
          --smooth SMOOTH       Smoothen the datapoints of frequencies, but reduce the details (integer, default=5)
        ```
        
        ## Snakemake workflow
        For streamlining nanopolish a Snakefile is included (using snakemake). The workflow uses a config file, of which an example is in this repository.
        
        ## Example data
        The `examples` folder contains calls and frequencies for the human ACTB gene from PromethION sequencing of NA19240. An example command is available.
        
        ## Companion scripts
        The `scripts` folder contains scripts for phasing modification calls in haplotypes based on [WhatsHap](https://whatshap.readthedocs.io/en/latest/) phasing, allele specific modification testing for phased data and differential modification testing across subjects.
        
        ## TO DO - CONTRIBUTIONS WELCOME
        - Outlier detection (in windows) across samples
        
Keywords: nanopore
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
Description-Content-Type: text/markdown
