all_against_ref file generation
Part : merge input data.
File : "lisez.moi" file, not yet registered
Why : For optmisation purpose, the file should be in starch format.
Proposition :
try this chunk of code:
source /softs/local/env/envbedops-2.4.15.sh
declare -r ASS_PATH=/groups/rapsodyn/Assembly
#----------------------------------------
for cul in $( loopOverCultivars bnapus echo )
do
align_file="$ASS_PATH/AlignOnRef/gs_bnapus_$cul/against_ref/$cul.tsv.gz"
zcat $align_file \
| perl -lane '$id = "'$cul'|$F[3]"; print join( "\t", @F[0..2],$id, @F[4..5] )' \
>> all_against_ref.tsv
done
sort-bed all_against_ref.tsv \
| starch - \
> all_against_ref.starch
Maybe it can be even faster considering inputs as starch file too.