Shell Programming and Scripting

 #!/bin/bash
        while true
	do
		printf "Is this a batch :"
		
        case "$id" in
        [yY])  echo "perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt 
                ;;
        [nN]) # code for X
                printf "Enter ID  : " ; read id # This has to be outside the case
                [ -z "$id" ] && break # This is not needed, $id will never contain a zero length
                [ "$id" = "end" ] && break # This is not needed. $id will never contain "end", here 
				echo ("perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo
                ;;
        end)  break ;;
        *)     ;; # Unknown option, do nothing
		esac
		printf "Is this a batch :"
	done