Metadata-Version: 2.1
Name: methplotlib
Version: 0.19.0
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)
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        # METHPLOTLIB
        
        This script generates a browser view on a window using data from  
        i) [nanopolish](https://github.com/jts/nanopolish), either as methylation calls or methylation frequencies (as processed by calculate_methylation_frequency.py). The methylation calls can additionally be phased using scripts/annotate_calls_by_phase.and scripts/split_calls_by_phase.py  
        ii) [nanocompore](https://github.com/tleonardi/nanocompore)  
        iii) in ont-cram format with MM/MP tags according to the SAM specifications and converted using e.g. [this script](https://github.com/kpalin/gcf52ref/blob/f5_to_usam/scripts/extract_methylation_fast5_to_sam.py)  
        iv) in bedgraph format  
        
        ## INSTALLATION
        `pip install methplotlib`
        
        ## USAGE
        ```
        methplotlib [-h] [-v] -m METHYLATION [METHYLATION ...] -n NAMES
                           [NAMES ...] -w WINDOW [-g GTF] [-b BED] [-f FASTA]
                           [--simplify] [--split] [--static STATIC] [--smooth SMOOTH]
                           [--dotsize DOTSIZE] [--example] [-o OUTFILE] [-q QCFILE]
        
        plotting nanopolish methylation calls or frequency
        
        optional arguments:
          -h, --help            show this help message and exit
          -v, --version         Print version and exit.
          -m, --methylation METHYLATION [METHYLATION ...]
                                data in nanopolish, nanocompore, ont-cram or bedgraph
                                format
          -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
          -f, --fasta FASTA     required when --window is an entire chromosome, contig or transcript
          --simplify            simplify annotation track to show genes rather than transcripts
          --split               split, rather than overlay the methylation tracks
          --static              Make a static image of the browser window (filename)
          --binary              Make the nanopolish plot ignorning log likelihood nuances
          --smooth              Rolling window size for averaging frequency values (int)
          --dotsize             Control the size of dots in the per read plots (int)
          --example             Show example command and exit.
          -o, --outfile OUTFILE File to write results to. Default:
                                methylation_browser_{chr}_{start}_{end}.html. Use
                                {region} as a shorthand for {chr}_{start}_{end} in the
                                filename. Missing paths will be created.
          -q, --qcfile QCFILE   File to write the qc report to. Default: The path in
                                outfile prefixed with qc_, default is qc_report_methyl
                                ation_browser_{chr}_{start}_{end}.html. Use {region}
                                as a shorthand for {chr}_{start}_{end} in the
                                filename. Missing paths will be created.
        
        ```
        
        ## 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
