dist-lz.sb

#!/bin/bash

#SBATCH --ntasks=1
#SBATCH --job-name=_dist-lz
#SBATCH --time=12:00:00
#SBATCH --partition=medium
#SBATCH --array=1-228%1
#SBATCH --output=snps/cojo/log/_dist-lz_%A_%a.out
#SBATCH --error=snps/cojo/log/_dist-lz_%A_%a.err
#SBATCH --export ALL

. /etc/profile.d/modules.sh
module load default-cardio slurm use.own python/2.7.5 R/3.4.2
export TMPDIR=/scratch/jhz22/tmp
export R_LIBS=

export p=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $1}' dist/INF1_nold.sentinels)
export chr=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $2}' dist/INF1_nold.sentinels)
export pos=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $3}' dist/INF1_nold.sentinels)
export r=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]+1{print $4}' dist/INF1_nold.sentinels)
export start=$(awk -vpos=${pos} 'BEGIN{if(pos <= 1e6) print 0; else print pos-1e6}')
export end=$(awk -vpos=${pos} 'BEGIN{print pos+1e6}')
(
   echo -e "MarkerName\tP-value\tWeight"
   gunzip -c METAL/${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],$12,$14}' | \
   sort -k1,1 | \
   join -12 -21 work/snp_pos - | \
   awk -vOFS="\t" '{print $2, $3, $4}'
) > dist/${p}-${r}.lz
cd dist
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 -