Open PAMorin opened 2 years ago
lindenb
commented
2 years ago @PAMorin I'm sorry I think I don't really understand the problem.
How about using a regular expression like
(scaffold_1|scaffold_2|scaffold_3|scaffold_4|scaffold_5|scaffold_10)
?
PAMorin
commented
2 years ago Thanks for the quick response!
It looks like you understood my problem (not understanding how to construct a multiple object expression) perfectly. This works:
chr="scaffold_4|scaffold_5|scaffold_10"
java -jar ${covplot}/dist/wgscoverageplotter.jar --dimension 1500x500 -C -1 --clip -R ${REFDIR}/${REF} ${BAMDIR}/${BAMFILE} --include-contig-regex ${chr} --percentile median > ${OUTDIR}/${BAMFILE}_covplot_allChrom.svg
The output is attached. My genome assembly has a few hundred scaffolds, but the first 22 are chromosome-length, and I only want to plot coverage of those scaffolds. This approach allows me to specify which ones to plot, and I can further refine it to omit or include a few specific scaffolds of interest in a single plot.
Thanks,
Phil
On 6/17/22 3:17 PM, Pierre Lindenbaum wrote:
@PAMorin https://github.com/PAMorin I'm sorry I think I don't really understand the problem.
How about using a regular expression like
|(scaffold_1|scaffold_2|scaffold_3|scaffold_4|scaffold_5|scaffold_10)|
?
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Subject of the issue
specify list of scaffolds for wgsCoveragePlotter
Your environment
Steps to reproduce
I want to plot coverage of only a specific subset of scaffolds, but all scaffolds are named sequentially (e.g., scaffold_1, scaffold_2, etc.). Is there a way to substitute a list variable or array for the --include-contig-regex regular expression:
e.g., chr=("scaffold_1" "scaffold_2" "scaffold_3" "scaffold_4" "scaffold_5" "scaffold_10") java -jar ${covplot}/dist/wgscoverageplotter.jar --dimension 1500x500 -C -1 --clip -R ${REFDIR}/${REF} ${BAMDIR}/${BAMFILE} --include-contig-regex ${chr} --percentile median > ${OUTDIR}/${BAMFILE}_covplot_allChrom.svg
Expected behaviour
WGS coverage plot with only the specified scaffolds
Actual behaviour
WGS coverage plot of only the first scaffold in the list $chr