do_step2.psh

#!/bin/bash

function do_step2 {
local gene=$1
echo $gene

cat ${gene}_?.st4 | sort -u | cut -d ' ' -f 1 | uniq -c > ${gene}.res
awk '$1==1 {print $2}' ${gene}.res > ${gene}.ok		# sequence specific chromosome :A for chr2 but C for chr6 and chrX 

awk '$1!=1 {print $2}' ${gene}_?.cand1 | sort -u > ${gene}.dup	# more chrs

sort -n ${gene}.ok ${gene}.dup | uniq -d > ${gene}.exc
sort -n ${gene}.ok ${gene}.exc | uniq -u > ${gene}.god 	# sequence specific chromosome: NGG for chrX

Rscript do_final.r "$gene"

}

do_step2 $1