Shell Programming and Scripting

name() {
	printf "\n\n"
	printf "Please enter the gene name  : "; read gene
	
	[ -z "$gene" ] &&
		printf "\n No ID supplied. Leaving match function." &&
		sleep 2 &&
		return
	[ "$gene" = "end" ] &&
		printf "\n Leaving match function." &&
		sleep 2 &&
		exit
	[ "$gene" != "GJB2 or MECP2 or PHOX2B" ] &&
		printf "\n That is not a target gene please use one of the formats listed." &&
		echo "
NM_003002.3:c.274G>T (reference transcript:coding change w/ nucleotide change)
chr11:g.111959693G>T (chromosome:genomic position w/ nucleotide change)
NC_000011.9:g.111959693G>T (Genebank accession #:genomic position w/ nucleotide change)"
	printf "Enter variant(s): "; IFS="," read -a variants

	code=""
	if [ "$gene" = "GJB2" ]
	then	code="NM_004004.5"
	elif [ "$gene" = "MECP2" ]
	then	code="NM_004992.3"
	elif [ "$gene" = "Phox2B" ]
	then	code="NM_003924.3"
	else	return
	fi
	for ((i = 0; i < ${#variants[@]}; i++))
	do	printf "%s:%s\n" "$code" "${variants[$i]}"
	done | tee -a c:/Users/cmccabe/Desktop/Python27/$gene.txt \
			>> c:/Users/cmccabe/Desktop/Python27/out.txt
}

 
code=""
	if [ "$gene" != "GJB2 or MECP2 or PHOX2B" ]
	then	code=printif ((i = 0; i < ${#variants[@]}; i++))
	                tee -a c:/Users/cmccabe/Desktop/Python27/$gene.txt \
			         >> c:/Users/cmccabe/Desktop/Python27/out.txt

case $gene in
	GJB2)
		code="NM_004004.5"
	;;
	MECP2)
		code="NM_004992.3"
	;;
	Phox2B)
		code="NM_003924.3"
	;;
	*) # everything else we do not won't to process.
		printf "%s \n" "This is not a target ..."
	;;
esac
printf "%s \n" "Enter variant(s): "
OLDIFS=$IFS
IFS=","
read -a variants
for (( i = 0; i < ${#variants[@]}; i++ ))
	do
	printf "%s %s\n" "$code" "${variants[$i]}" # is plain redirection ok here instead of using tee ?
	done
IFS=$OLDIFS