Shell Programming and Scripting

 awk '{if (f==1) { r[$3] } else if (! ($3 in r)) { print $1 } } ' f=1 ${id}_name.txt f=2 $(id}.txt

awk '/variantchecker/ {r[$1]} FNR==NR {next} !($1 in r)' /tmp/GJB2_name.txt /tmp/GJB2.txt
NM_004004.5:c.283G>T

 check() {
    printf "\n\n"
	awk 'NR>1 { if ($2 ~ /^\(/ ) {$1=""; print "Found error: ", $0} else { sub(/.*:/, "", $1); sub(/.*:/, "", $7); print "No error: " $1 "," $7}}' C:/Users/cmccabe/Desktop/Python27/${id}_name.txt
	printf "Is the variant correct?  Y/N "; read match_choice
	
    case "$match_choice" in
        [yY]) id="${id}"; additionalg ;; 
        [nN]) cd 'C:/Users/cmccabe/Desktop/Python27/' awk '/variantchecker/ {r[$1]} FNR==NR {next} !($1 in r)' ${id}_name.txt ${id}.txt; gjb2 ;;  
    esac
}

 
Found error:   (variantchecker): G not found at position 289, found T instead.
No error: c.79G>A,p.(Val27Ile)
Is the variant correct?  Y/N

 check() {
    printf "\n\n"
	awk 'NR>1 { if ($2 ~ /^\(/ ) {$1=""; print "Found error: ", $0} else { sub(/.*:/, "", $1); sub(/.*:/, "", $7); print "No error: " $1 "," $7}}' C:/Users/cmccabe/Desktop/Python27/${id}_name.txt
	printf "Is the variant correct?  Y/N "; read match_choice
	
    case "$match_choice" in
        [yY]) id="${id}"; additionalg ;; 
        [nN]) cd 'C:' C:/Users/cmccabe/Desktop/Python27/; awk '/variantchecker/ {r[$1]} FNR==NR {next} !($1 in r)' "${id}"_name.txt "${id}".txt; gjb2 ;;  
    esac
}

 
Found error:   (variantchecker): G not found at position 289, found T instead.
Is the variant correct?  Y/N n
awk: fatal: cannot open file `gj_name.txt' for reading (No such file or director
y)

 check() {
    printf "\n\n"
	awk 'NR>1 { if ($2 ~ /^\(/ ) {$1=""; print "Found error: ", $0} else { sub(/.*:/, "", $1); sub(/.*:/, "", $7); print "No error: " $1 "," $7}}' C:/Users/cmccabe/Desktop/Python27/${id}_name.txt
	printf "Is the variant correct?  Y/N "; read match_choice
	
    case "$match_choice" in
        [yY]) id="${id}"; additionalg ;; 
        [nN]) id="$id"; cd 'C:' C:/Users/cmccabe/Desktop/Python27/; awk '/variantchecker/ {r[$1]} FNR==NR {next} !($1 in r)' C:/Users/cmccabe/Desktop/Python27/${id}_name.txt C:/Users/cmccabe/Desktop/Python27/${id}.txt; gjb2 ;;
    esac
}