lz.sb

#!/bin/bash

#SBATCH --ntasks=1
#SBATCH --job-name=_lz
#SBATCH --time=12:00:00
#SBATCH --partition=skylake
#SBATCH --array=1-180%1
#SBATCH --output=/rds/user/jhz22/hpc-work/work/_lz_%A_%a.out
#SBATCH --error=/rds/user/jhz22/hpc-work/work/_lz_%A_%a.err
#SBATCH --export ALL

export list=work/INF1.merge
export p=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $5}' ${list})
export r=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $6}' ${list})
export chr=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $8}' ${list})
export pos=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $9}' ${list})
export Start=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $2}' ${list})
export End=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $3}' ${list})
export flanking=1e6
export start=$(awk -vpos=${Start} -vflanking=${flanking} 'BEGIN{start=pos-flanking;if(start<0) start=0;print start}')
export end=$(awk -vpos=${End} -vflanking=${flanking} 'BEGIN{print pos+flanking}')

(
   echo -e "MarkerName\tP-value\tWeight"
   gunzip -c METAL/${p}-1.tbl.gz | \
   awk -vOFS="\t" -vchr=${chr} -vpos=${pos} -vstart=${start} -vend=${end} \
       '($1 == chr && $2 >= start && $2 < end){split($3,a,"_");print a[1],10^($12),$18}' | \
   sort -k1,1 | \
   join -12 -21 work/snp_pos - | \
   awk -vOFS="\t" '{print $2, $3, $4}'
) > work/${p}-${r}.lz
cd work
rm -f ld_cache.db
locuszoom-1.4 --source 1000G_Nov2014 --build hg19 --pop EUR --metal ${p}-${r}.lz \
              --plotonly --chr $chr --start $start --end $end --no-date --rundir .
mv chr${chr}_${start}-${end}.pdf ${p}-${r}.lz.pdf
pdftopng -r 300 ${p}-${r}.lz.pdf ${p}-${r}
mv ${p}-${r}-000001.png ${p}-${r}.lz-1.png
mv ${p}-${r}-000002.png ${p}-${r}.lz-2.png
cd -