Shell Programming and Scripting

annovar() {
    # combine id and position files
	cd 'C:\Users\cmccabe\Desktop\annovar'
	cp out_parse.txt "$(cat target.txt)"
	
	# run annotation
              $( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f ")' < target.txt )
			  
     printf "The annotation is complete, would you like analyze additional target gene patients? Y/N "; read match_choice
	 case "$match_choice" in
        [yY]) id="${id}"; menu ;;
        [nN]) id="${id}"; remove ;;
		esac
}

 
countdown=operation # there are (6) after the -operation
while [[ ${countdown} -ge 0 ]]
do
        echo ${countdown}
        sleep 1
        countdown=$(( ${countdown} - 1 ))
done 
Time until Completion = "${countdown}"