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methplotlib

(★ 96)

Plotting tools for nanopore methylation data

파일 탐색기

최종 버전 다운로드 (.zip)

- - publish.yml
  - python-package-conda.yml
- dependabot.yml
- DNase_cluster_ACTB.bed.gz
- GRCh38-ACTB-locus.gtf.gz
- NA19240-methylation_ACTB_calls.tsv.gz
- NA19240-methylation_ACTB_frequency.tsv.gz
- test.sh
- assoc_hap_meth.py
- merge_simplified_meths.py
- paircor.py
- per_read_methylation.py
- plot_hap_meth.py
- plot_methylation_per_allele.py
- plot_methylation_per_allele_2.py
- simplify_haplotype_specific_meth.py
- - __init__.py
  - differential.py
- - ACTB_calls.tsv.gz
  - DNAse_cluster.bed.gz
  - g38_locus.gtf.gz
  - meth_freq.tsv.gz
  - test.sh
- __init__.py
- annotation.py
- helpers.py
- import_methylation.py
- methplotlib.py
- plots.py
- qc.py
- utils.py
- version.py
- allele_specific_modification
- annotate_calls_by_phase.py
- calculate_methylation_frequency.py
- differential_modification
- split_calls_by_phase.py
- chr21.bed.gz
- d1.tsv.gz
- d2.tsv.gz
- result.txt
- result_diff.tsv.gz
- test_differential.py
.gitignore
.travis.yml
config_example.yaml
CONTRIBUTORS
LICENSE
MANIFEST.in
README.md
setup.py
Snakefile

# 설치 가이드

1. 코드 내려받기

git clone https://github.com/wdecoster/methplotlib

깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.

cd methplotlib

방금 내려받은 프로젝트 폴더 안으로 이동합니다.

2. Python

쉬움 추천

사전 준비물

Git GitHub에서 프로젝트 코드를 내려받으려면 필요합니다.
Python 3 설치 시 'Add Python to PATH' 옵션을 꼭 체크하세요 (Windows).

pip install .

PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.

python <실행할 파일명>.py # README에서 정확한 실행 파일명을 확인하세요

파이썬 스크립트(또는 모듈)를 실행합니다.

✅ 에러 메시지 없이 실행되고 터미널에 안내 문구가 출력되면 정상입니다.

// repository documentation

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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.py and scripts/split_calls_by_phase.py  
ii) [nanocompore](https://github.com/tleonardi/nanocompore)  
iii) in ont-cram format with MM/ML tags according to the SAM specifications  
iv) in bedgraph format, with 4 columns (chromosome, start, end, value) or the 5 columns written by `modkit pileup --bedgraph`  
v) in bedMethyl format, as written by [modkit](https://github.com/nanoporetech/modkit) `pileup` (18 columns, with or without `--only-tabs`) or by `modbam2bed --extended` (14 columns). Files containing multiple modifications (e.g. 5mC and 5hmC) do not have to be split up: each modification gets its own track, and `--mods` can be used to restrict to some of them

## INSTALLATION

Creating a new conda environment:  
`conda create -n methplotlib methplotlib`

Or using pip:  
`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