UNIX for Advanced & Expert Users

ID1|VAR2|VAR3|VAR4|VAR5
ID2|VAR2|VAR3|PART1;PART2|1;2
ID3|VAR2|VAR3|A, B, C;PART2;BEFORE LF\nAFTER LF|1;2;3
ID4|VAR2|VAR3|1;2;3,;4|1;2;3;4

D1|VAR4
ID2|PART1
ID2|PART2
ID3|A, B, C
ID3|PART2
ID3|BEFORE LF  AFTER LF
ID4|1
ID4|2
ID4|3
ID4|4

awk -F"|" '{ print $1f"|"$4F }' < patienttest2.txt | sed 's/,/comma/g' | sed 's/|/,/' | sed 's/;/,/g' | awk -F , '{for (i=2;i<=NF;i++) if ($i>=0) print $1 FS $i}' | sed 's/co
mma/,/g' |

awk '
BEGIN {	FS = OFS = "|"
}
{	while(NF < 5) {
		if(NF <= 1) {
			# Read a continuation line for field 5 or 1st line
			# of next record.
			if(getline != 1) {
				# Break out on EOF
				break
			}
		} else {# Read continuation line for field 4.
			if((getline x) != 1) {
				# We should not hit EOF in the middle of a
				# continued line, but check for it anyway.
				break
			}
			$0 = $0 " " x	# Replace incorrect <newline> with a
					# space.
			$1 = $1		# Reset NF after combining lines.
		}
	}
	# Discard <carriage-return>s.
	gsub(/\r/, "")
	n = split($4, sf, ";")
	for(i = 1; i <= n; i++)
		print $1, sf[i]
}' patienttest2.txt

ID1|VAR2|VAR3|VAR4|VAR5
ID2|VAR2|VAR3|PART1;PART2|1;2
ID3|VAR2|VAR3|A, B, C;PART2;BEFORE LF
AFTER LF|1;2;3
ID4|VAR2|VAR3|1;2;3,;4|1;2;3;4
ID5|VAR2|VAR3|1,
2;3
4;5
6|f5
f6
f7
ID6|VAR2|VAR3|A,b;C,d|a
con

ID1|VAR4
ID2|PART1
ID2|PART2
ID3|A, B, C
ID3|PART2
ID3|BEFORE LF AFTER LF
ID4|1
ID4|2
ID4|3,
ID4|4
ID5|1, 2
ID5|3 4
ID5|5 6
ID6|A,b
ID6|C,d