tolkit
tidk plot doesn't work.
I generated the tsv file, which the program didn't work before, and now the program is complaining and not working again. I wanted to generate the plot and I got an error now. My code is basically a modification of the one on the main page.
tidk plot **-o JC_TR -h 120 -w 800 -t JC_telomeric_repeat_windows.tsv**
According to the program itself:
Usage: tidk plot [OPTIONS] --tsv <TSV>
Options:
-t, --tsv <TSV> The input TSV file
--height [<HEIGHT>] The height of subplots (px). [default: 200]
-w, --width [<WIDTH>] The width of plot (px) [default: 1000]
-o, --output [<OUTPUT>] Output filename for the SVG (without extension) [default: tidk-plot]
--fontsize [<FONT_SIZE>] The font size of the axis labels in the plot [default: 12]
--strokewidth [<STROKE_WIDTH>] The stroke width of the line graph in the plot [default: 2]
-h, --help Print help
-V, --version Print version
SVG plot of TSV generated from tidk search.
I don't understand why the program is so miserable. I am including all the parameters, yet it doesn't run now. I first put the tsv parameter at the beginning (as written on the main page), and since it didn't work then I thought it might be complaining about parameter order. So I moved it to the end as in USAGE and it doesn't work either.
Why is it not working now? All the parameters have defaults, it shouldn't complain.
The tidk command is already there:
tidk plot -o 176-TR -h 120 -w 800 -t Scaff_telomeric_repeat_windows.tsv
Before that is basic conda activation for running:
# Init conda
source /data/common/apps/conda_init.sh
which conda
#activate conda environment
conda activate genomics
# Save starting time
start_time=$(date +%s)
echo "TR visualization : test: Job started: $(date)"
cd /data/common/user/analysis/genomeQC/
Version= (genomics) [user@pirate genomeQC]$ tidk -V tidk 0.2.65
Running in conda