Suggestion to improve --BED option

[marcusnygaard]

I am a very avid user of your nice tool :)

I often need to plot 40-50 genes at a time, and typically do so using the --BED parameter to plot many regions, however, the filename prefixes are not super useful (coordinates), and my bed file actually has a 4th info column

My beds typically look like:
chrx 123 345 Leptin_Locus
chry 678 425 Lpl_Locus

The resulting filenames just become (given -out Plot.png) chry:678-425_Plot-png

It would be amazing if any optional info fourth column also got added as a prefix to the resulting file!

[lldelisle]

Hi @marcusnygaard ,
I fully agree with you... The trick I am doing now is this one:

ini_file=whatever.ini
bed_file=whatever.bed
extension=pdf
pgt --BED ${bed_file} --tracks ${ini_file} -o ${ini_file/.ini/.${extension}}
# I rename the outputs
while read l; do
    chrom=$(echo $l | awk '{print $1}')
    start=$(echo $l | awk '{print $2}')
    end=$(echo $l | awk '{print $3}')
    locus_name=$(echo $l | awk '{print $4}')
    mv ${ini_file/.ini/}_${chrom}-${start}-${end}.${extension} ${ini_file/.ini/}_${locus_name}.${extension} 
done < ${bed_file}

I hope this helps you.