About chrVis

chrVis is a chromosome visualization tool, aims to facilitate the identification and analysis of linkage blocks, chromosome structure and differences from comparisons of chromosomes. Our tool is effective in displaying variation in chromosome structure and, generally, any other kind of positional blocks on the chromosome intervals.

TODO

• Image auto Size
• Legend support
• Block name auto arrangement
• Symbols or glyph mark support
• Links between chromosomes
• Tutorials and Samples

Requirements

The script requires python module : svgwrite

install with pip:

pip install svgwrite`

sample command line

python App.py --conf sample.conf --out sample_out.svg

Usage

usage: App.py [-h] [-c CONF] [-o OUT]

optional arguments:
  -h, --help            show this help message and exit
  -c CONF, --conf CONF  configure file
  -o OUT, --out OUT     output filename

sample configure file

[general]
karyotype = sample_chr.txt
bandfile = sample_gene.txt

scale = 50000
imgWidth = 1200
imgHeight = 600

[ideogram]
thickness = 20
spacing = 80
fill      = yes
label_size = 20

[band]
alpha = 1
thickness = 10
show_name = True

sample karyotype file

Three columns chromosome ID,chromesome name , chromosome length, chromosome color

chr1  My.Chr1 28954470  #333300
chr2  My.Chr2 30652350  #333300
chr3  My.Chr3 25211582  #333300
chr4  My.Chr4 29556843  #333300
chr5  My.Chr5 24787886  #333300
chr6  My.Chr6 22802870  #333300
chr7  My.Chr7 11041128  #333300
chr8  My.Chr8 18570557  #333300
chr9  My.Chr9 28466655  #333300
chr10 My.Chr10  17444910  #333300
chr11 My.Chr11  18674527  #333300
chr12 My.Chr12  23362826  #333300
chr13 My.Chr13  19446246  #333300

sample bandfile file

Five columns chromosome name , band name,band start,band end, fill color

chr1  block0  18655440  19004551  #bacac6
chr4  block63 21300577  21681252  #bacac6
chr4  block64 19835040  21134129  #bacac6
chr4  block65 24342697  25086406  #00bc12
chr5  block73 15698017  17228364  #00bc12
chr5  block74 19286756  20060843  #00bc12
chr5  block75 14726663  15515996  #00bc12
chr5  block76 18302344  19240018  #00bc12
chr5  block77 20273832  20935547  #00bc12
chr10 block11 0 17444910  #0eb83a
chr6  block84 2855768 3460898 #0eb83a
chr8  block91 10654172  11720140  #0eb83a
chr8  block92 11768805  12802006  #0eb83a
chr8  block93 10394348  10605509  #0eb83a
chr11 block18 14537869  15203608  #16a951
chr3  block55 10019219  11003401  #16a951
chr6  block85 16028585  17345205  #16a951
chr4  block66 13980220  14717750  #f35336
chr4  block67 13448043  13874835  #f35336
chr4  block68 12779674  13388859  #f35336
chr9  block96 13165043  14384072  #f35336
chr9  block97 11152423  12218998  #f35336
chr9  block98 12392176  13083726  #f35336

sample output