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#Input are: list of all metal output files (one per line) and locations of SNPs

 qsub -t1 -l walltime=00:20:00 make_locuszoom.qsub -d $workingdir -e errandout/ -o errandout/ -F "-l phase3.locations2 -d metal_outputsB.txt"

#!/bin/bash
#PBS -V

while getopts l:d: option
do
  case "${option}"
    in
      l) snplocations=${OPTARG};;
      d) lzresults_list=${OPTARG};;   
    esac
done

#Load R
module load R 
#Take the line of metal results
lzresults=$(awk -v lineno=$PBS_ARRAYID '{if (NR == lineno) print }' $lzresults_list )

echo "Filtering data to columns 1 and 6 (metal defaults)."
 cut -f 1,6 results_cat/$lzresults | LC_ALL=C sort -k1,1b > "$lzresults".temp.txt

echo "Joining to reference locations"
 LC_ALL=C join $snplocations "$lzresults".temp.txt > "$lzresults".lz

echo MarkerName P.value > lz.header

#for each chromosome, make a file (will be parsable)
for chr in {1..22}
do
 echo "printing results for $chr"
 awk -v chr=$chr '{if ($2 == chr) print $1,$4}' "$lzresults".lz  > results_lz/"$lzresults"."$chr".lz
done

echo "Cleanup"
 #rm "$lzresults".temp.txt
 #rm "$lzresults".lz