circDraw-py

This is a stand alone project which extends the power of circDraw service. To better connect with the upsteam pipline, we create a python3 package for generating publication quality visualization of circRNA with internal structures and modifications/functional elements information. And to access circDraw webservice without a browser, a command line inferface is integrated into for you to submit jobs in shell. Overall, this repo contains the following:

1. Python package for circDraw visualization
2. circDraw upload command line tool for webservice

Installation

Install via pip

pip3 install circDraw

Install via source code

Clone the github repo or unzip the source code, run the following command at the root of circDraw-py directory:

bash install.sh

Dependency

• Python 3.6.5
• Matplotlib 3.1.2
• Numpy 1.18.0
• Colour 0.1.5
• Requests 2.22.0

Usage: Draw with circDraw

CircDraw provides python package to use when drawing circular RNA with the emphasis on backspliting sites visulization and epigenetic/SNP marker display. Import circDraw class via your favourite python3 interpreter or enbed it inside a script to use the drawing function.

from circDraw import circDraw

 # initiate a circDraw instance
cd = circDraw()

# set color of circ_on_chr (optional)
cd.set_palette(["#5CA0F2", "#FF881D", '#e30067', '#924900','#ab9c00','#ccd0d2', '#075800', '#5e0094',])

# set color of modifications (optional)
mod_palette = {'m6a': '#E98B2A',
               'm5c': '#E16B8C',
               'm1a': '#64363C',
               'pu': '#ffa12c',
               '2ome': '#1a6f00',
               'mre': '#6D2E5B',
               'rbp': "#2B5F75",
               'orf': '#516E41'}
cd.set_mod_palette(mod_palette)

# draw backsplicing site on chromosome region
cd.circ_on_chr('/path/to/file')

# draw modifications on circRNA
cd.mod_on_circ('/path/to/file')

Method

circ_on_chr

circDraw.circ_on_chr(file, title='circDraw', dpi=300, save='png', show=True, size=(10, 5))

• File:

  • Only supported 'csv'

  • Start	End	Type	Name	Color (Optional)

  • Start < End

  • Type: circ, exon, intron, gene

  • Color: RGB, RGBA, hex, or supported color names.

• Title: The title of the plot

• Save: file format you wish to save as, PNG, PDF, JPEG, etc.

• Show: Bool, wheather to show the plot after rendering.

• Size: (Length, Width) the size of the plot.

mod_on_circ

circDraw.mod_on_circ(self, file, dpi=100, save='png', show=True, size=(7, 7), sep_mod=False)

• File:

  • Only supported 'csv'

  • Start	End	Type	Name	Color (Optional)

  • Start < End

  • Type: circ, exon, intron, and modifications type

    • Modifications type: m6A, m1A, m5C, pU, 2OMe, MRE, RBP, ORF

  • Color: RGB, RGBA, hex, or supported color names.

• Save: file format you wish to save as, PNG, PDF, JPEG, etc.

• Show: Bool, wheather to show the plot after rendering.

• Size: (Length, Width) the size of the plot.

• sep_mod: Bool, prevent the modifications from overlapping if set True.

set_palette

circDraw.set_palette(palette)

A list of colors, the length of the list must bigger than 5.

set_mod_palette

circDraw.set_mod_palette(palette)

A dictionary of colors match with the modification. You can change any one of the modification colors.

Usage: Upload to circDraw webservice

Upload on command line

1. Upload files with parameters

• Single upload file

$ circDraw-upload -f test_circfile.bed -t BED -s human-hg19

• Multiple upload files

$ circDraw-upload -f test_circfile.bed -t BED -s human-hg19 -f test_circfile.bed -t BED -s human-hg19

2. Upload file with init file

circDraw-upload also supports upload file from one init file to avoid tedious typing through command line. You can specify the uploaded filename, file type and its origin species in a single csv file. The cvs file should follow the following format with "," seperating each column:

Note: Currently circDraw only supports limited filetypes and species, they are specified in the following table:

• Supported file types:

• Supported Species

• Single upload file

$ circDraw-upload -i test_init_single.txt

• Multiple upload files

$ circDraw-upload -i test_init_multiple.txt

Help

$ circDraw-upload -h
$ circDraw-upload --help

usage: circDraw-upload [-h] [-f FILE] [-t {BED,CIRI}]
                       [-s {human-hg19,human-hg38,mouse-mm10,rat-rn6,yeast-sacCer3,zebra-fish-danRer11}]
                       [-i INITFILE]

Upload command line interface for circDraw web server.

optional arguments:
  -h, --help            show this help message and exit
  -f FILE, --file FILE  Filename you want to upload.
  -t {BED,CIRI}, --type {BED,CIRI}
                        Filetype of your file, circDraw currently supports
                        ['BED', 'CIRI']. Names of the selected file type
                        should be exactly matched.
  -s {human-hg19,human-hg38,mouse-mm10,rat-rn6,yeast-sacCer3,zebra-fish-danRer11}, --species {human-hg19,human-hg38,mouse-mm10,rat-rn6,yeast-sacCer3,zebra-fish-danRer11}
                        Specify your species, currently circDraw support
                        ['human-hg19', 'human-hg38', 'mouse-mm10', 'rat-rn6',
                        'yeast-sacCer3', 'zebra-fish-danRer11']. Names of the
                        species should be exactly matched.
  -i INITFILE, --initfile INITFILE
                          header filename which specify the information of
                        uploaded filename, uploaded filetype and corresponding
                        species; File should be in csv format where each row
                        represents a file, and three column should be
                        (filename, filetype, species). Note that this mode
                        overwrites any '-f', '-t', '-s' input.

More information

This a part of circDraw project. Please visit our Contact page if you have any questions.

Copyright: Qu Lab, School of Life Science, Sun Yat-sen University, Guangzhou, CHINA.