Download this repository. And then
cd nucle
python3 setup.py install
Python tools for nucleome browser.
include following functions:
usage: nucle [-h] [-v]
{hssinfo,servehss,cmm2nucle3d,hss2nucle3d,createdatasheet} ...
python tools for nucleome browser
positional arguments:
{hssinfo,servehss,cmm2nucle3d,hss2nucle3d,createdatasheet}
subcommand help
hssinfo output basic info about hss file
servehss host a hss file as web data service
cmm2nucle3d convert cmm format to nucle3d format
hss2nucle3d extract a structure in a hss file and output it as
nucle3d format
createdatasheet download data from 4DN data portal and prepare a input
data sheet for nucleserver
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
nucle3d format is used in Nucleome Browser Chromosome 3D Structure viewer web component.
Generate a nucle3d format file and put it in a web server. Make sure that the URL can accessed by "http(s)://vis.nucleome.org"
(set its header "CORS").
In nucleserver, we provide a subcommand to start a simple web server with CORS Header "Access-Control-Allow-Origin: https://vis.nucleome.org". For example , if you have a nucle3d format file /home/yourname/data/file.nucle3d. you can start a file web server using our tool nucleserver
nucleserver file -r /home/yourname/data
It will start a server http://127.0.0.1:8611 and the nucle3d file url will be http://127.0.0.1:8611/get/file.nucle3d. Then, input this file URL in Nucleome Browser Chromosome 3D Structure viewer. The 3D structure will be shown in this panel. If 8611 port is occupied by another nucleserver program or other program. You can start with -p parameter to set this web service to another port.
version 0.0.1
TITLE [NAME] # Tab split
GENOME hg38 # Tab split
BINSIZE [binsize]
CHR chr1 # Tab split
i,x,y,z
i,x,y,z
..
CHR chr2
..
i is 0-index, gap of index i permitted