Making gene annotation file to draw regional plots for GWAS, a shell script

for i in {{1..22},"X","Y"}

do

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 
 -e 'select distinct name, chrom, txStart, txEnd,strand, 
 name2, IF(NOT(txEnd<248956422 OR txStart>1),0, 
IF(txStart>1,txStart-1,248956422-txEnd)) as distance 
 from refGene where chrom="chr'$i'" order by distance' > temp1

sort -u -n -k 3,3 -k 4,4 -s temp1 >temp2

rm -fr temp1

echo "START STOP SIZE STRAND GENE" >"chr"$i"_hg18.txt"

awk '{print $3,$4,$4-$3,$5,$6}' temp2 | sed '1d;$d' >> "chr"$i"_hg18.txt"

echo "Done with chr$i"

rm -fr temp2

done