Shell Programming and Scripting

 #!/bin/bash
while true
do
        printf "Is this a batch  : " ; read id
        [ -z "$id" ] && break
If "$id" = Y, Then
        [ "$id" = "end" ] && break
        perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt 
Else
      If "$id" = N, Then 
      printf "Enter ID  : " ; read id
      [ -z "$id" ] && break
      [ "$id" = "end" ] && break
      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
done

if [ "$id" = "Y" ]
then
        echo "do something
elif [ "$id" = "N" ]
then
        echo "do something else"
else
        echo "unknown option"
fi

case "$id" in
[yY])
        echo "do something"
        ;;
[nN])
        echo "do something else"
        ;;
end)
        break
        ;;
)
        break
        ;;
*)
        echo "Unknown option"
        ;;
esac

If "$id" = Y, Then
        [ "$id" = "end" ] && break

 #!/bin/bash
while true
do
        printf "Is this a batch  : " ; read id
        [ -z "$id" ] && break
        [ "$id" = "end" ] && break
case "$id" in
[yY])
        echo "perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt"
        ;;
[nN])
        printif "Enter ID : ' ; read id
		[ -z "$id" ] && break
        [ "$id" = "end" ] && break
        ;;
end)
       
	    ;;
)	  

	    ;;
*)
        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"
	    ;;
esac
done

  bash ~/test.sh
/home/cmccabe/test.sh: line 7: syntax error near unexpected token `$'in\r''
'home/cmccabe/test.sh: line 7: `case "$id" in

tr -d '\r' < windowstext > unixtext

printf "Is this a batch :"
while read id
do
        case "$id" in
        [yY]) echo perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt 
                ;;
        [nN]) # code for X
                printf "Enter ID  : " ; read id
                [ -z "$id" ] && break
                [ "$id" = "end" ] && break
                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

 #!/bin/bash
while true
do
        printf "Is this a batch :"
while read id
do
        case "$id" in
        [yY]) echo perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt 
                ;;
        [nN]) # code for X
                printf "Enter ID  : " ; read id
                [ -z "$id" ] && break
                [ "$id" = "end" ] && break
                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

  bash ~/test.sh
/home/cmccabe/test.sh: line 22: syntax error: unexpected end of file

 printf "Is this a batch :"