This tool can be used to script the taking of screenshots with IGV.
It can be used either locally on your PC (as a background task, without sacrificing your monitor), or
even in completely headless environments such as compute clusters (for example, if your desktop isn't allowed
direct access to secured data).
It achieves this by using the "X virtual frame buffer", Xvfb
In case you do not have a local IGV/Xvfb installation on the relevant machines, we also provide an IGV_xfvb Docker/Singularity image for easy containerisation.
For Singularity
- working singularity installation
- python3
- .igv folder in the home directory of the current user
or on your local computer
- full igv installation
xvfb-run
installed and in$PATH
- python3
The image IGV_xfvb Image can be pulled and formated to singularity format using:
singularity pull docker://stephanholgerdrukewitz/igvplots:latest
- Main entry point is the
plotRegions.py
script plotRegions
processes avars.tsv
'todo list'.- The actual work is done inside
PlotVarSingularity()
orPlotVarIGVlocal()
funtions from the igvXfvb.py script - both functions need an ID, chro, start, end, mapping, key
- The actual work is done inside
- The
vars.tsv
filechro
,start
,end
,mapping
, are informations about the alignment file and the position of interestID
andkey
are only uysed in the naming of the output, could be removed in future
- both
plotVar
-functions write a 'plot.bat' file which is later read in by igvXfvb - plots are saved in a directory with the name
Snaphots
in your current working directory - every variant provided to PlotVarSingularity or PlotVarIGVlocal is plotted 3 times --> 30nt to both sides, 75nt to both sides, 150nt to both sides
- PlotVarSingularity or PlotVarIGVlocal both call igv headless using :
xvfb-run --auto-servernum --server-num=1 java -Xmx8000m jar /opt/conda/bin/igv.jar -b plot.bat
- /opt/conda/bin/igv.jar is the location of the igv.jar file in the docker image, might differ depending on your installation
This is an example plot.bat
, created from the first line of the provided in vars.tsv.
See also the pseudocode in plotRegions.py
, which reads out vars.tsv
and calls PlotVarSingularity
or PlotVarIGVlocal
new
maxPanelHeight 5000
genome hg19
snapshotDirectory Snapshots
load /mnt/pat2.bam
group strand
goto chr2:41196281-41196341
sort base
collapse
snapshot Patient2_pat2_brcaBlaBlub_pat2_out_pad30_collapse.png
expand
snapshot Patient2_pat2_brcaBlaBlub_pat2_out_pad30_expand.png
goto chr2:41196236-41196386
sort base
collapse
snapshot Patient2_pat2_brcaBlaBlub_pat2_out_pad75_collapse.png
expand
snapshot Patient2_pat2_brcaBlaBlub_pat2_out_pad75_expand.png
goto chr2:41196161-41196461
sort base
collapse
snapshot Patient2_pat2_brcaBlaBlub_pat2_out_pad150_collapse.png
expand
snapshot Patient2_pat2_brcaBlaBlub_pat2_out_pad150_expand.png
exit
Stephan drukewitz --> [email protected] --> [email protected]