Download this repository and then run the following script.
cd nucle
python3 setup.py install
Various functions to support visualization of 3D genome structure models in 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 an 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 for displaying 3D genome structure models. You can create a nucle3d format file and put it in a web server. Make sure that the URL can be accessed by "http(s)://vis.nucleome.org" by setting its header "CORS".
In nucleserver, we also 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/folder/file.nucle3d. you can start a file web server using our tool nucleserver with the following script.
nucleserver file -r /home/yourname/folder
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, paste this URL in Nucleome Browser 3D genome structure model viewer. The 3D model will be shown in this panel. If 8611 port is occupied by another 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
..
Note that the genome coordinates i is 0-index and gaps of index i are also permitted.