macでインフォマティクス

macでインフォマティクス

NGS関連のインフォマティクス情報についてまとめています。

pyGenomeTracks

 

pyGenomeTracksは、高度にカスタマイズ可能な高品質のゲノムブラウザトラックを作成することを目的としている。Hi-Cデータの他、以下のデータからplotを作成することが可能になっている。

  • bigwig
  • bed/gtf (many options)
  • bedgraph
  • epilogos
  • narrow peaks
  • links (represented as arcs)
  • Hi-C matrices

 

Documentation

example

 

インストール

依存

  • Python >=3.6
  • numpy >= 1.16
  • intervaltree >=2.1.0
  • pyBigWig >= 0.3.4
  • hicmatrix >= 0.14
  • pysam >= 0.8
  • matplotlib >= 3.1.1
  • gffutils >=0.9

本体 Github

https://github.com/deeptools/pyGenomeTracks

#bioconda (link)
conda create -n pygenometracks-env -y
conda activate pygenometracks-env
conda install -c bioconda -c conda-forge pygenometracks

#pip
pip install pyGenomeTracks

pygenometracks -h

$ pygenometracks -h

usage: pygenometracks --tracks tracks.ini --region chr1:1000000-4000000 -o image.png

 

Plots genomic tracks on specified region(s). Citation : Ramirez et al. High-

resolution TADs reveal DNA sequences underlying genome organization in flies.

Nature Communications (2018) doi:10.1038/s41467-017-02525-w

 

optional arguments:

  -h, --help            show this help message and exit

  --tracks TRACKS       File containing the instructions to plot the tracks.

                        The tracks.ini file can be genarated using the

                        `make_tracks_file` program.

  --region REGION       Region to plot, the format is chr:start-end

  --BED BED             Instead of a region, a file containing the regions to

                        plot, in BED format, can be given. If this is the

                        case, multiple files will be created using a prefix

                        the value of --outFileName

  --width WIDTH         figure width in centimeters

  --height HEIGHT       Figure height in centimeters. If not given, the figure

                        height is computed based on the heights of the tracks.

                        If given, the track height are proportionally scaled

                        to match the desired figure height.

  --title TITLE, -t TITLE

                        Plot title

  --outFileName OUTFILENAME, -out OUTFILENAME

                        File name to save the image, file prefix in case

                        multiple images are stored

  --fontSize FONTSIZE   Font size for the labels of the plot

  --dpi DPI             Resolution for the image in case the ouput is a raster

                        graphics image (e.g png, jpg)

  --trackLabelFraction TRACKLABELFRACTION

                        By default the space dedicated to the track labels is

                        0.05 of the plot width. This fraction can be changed

                        with this parameter if needed.

  --trackLabelHAlign {left,right,center}

                        By default, the horizontal alignment of the track

                        labels is left. This alignemnt can be changed to right

                        or center.

  --version             show program's version number and exit

 

 

実行方法

1、trackファイルの作成

git clone https://github.com/deeptools/pyGenomeTracks.git
cd pyGenomeTracks/examples/
make_tracks_file --trackFiles input1.bed input2.bw -o tracks.ini

2、trackファイルと描画領域を指定してpyGenomeTracksを実行

pyGenomeTracks --tracks track.ini --region chr1:1000-20000 -o bigwig.png

 

 

テストラン

exampleランのコードをそのまま走らせてみる。

pyGenomeTracks --tracks bigwig_track.ini --region X:2,500,000-3,000,000 -o bigwig.png

f:id:kazumaxneo:20200330225924p:plain

 

pyGenomeTracks --tracks bigwig_with_genes.ini --region X:2,800,000-3,100,000 -o bigwig_with_genes.png 

f:id:kazumaxneo:20200330230018p:plain

 

pyGenomeTracks --tracks narrow_peak2.ini --region X:2760000-2802000 --trackLabelFraction 0.2 --dpi 130 -o master_narrowPeak23.png

f:id:kazumaxneo:20200330230223p:plain

 

pyGenomeTracks --tracks hic_track.ini -o hic_track.png --region chrX:2500000-3500000

f:id:kazumaxneo:20200330230355p:plain

 

引用

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A. Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar & Thomas Manke
Nature Communications volume 9, Article number: 189 (2018)

 

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