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if you need to "fold" the lines at 60 char width, pipe the output to fold:
awk .... | fold -w 60

Try alsoawk '
NR==FNR {PAT[$1,$2,$3]
next
}
{IX = $1
L1 = length ($1) + 1
$1 = $1 "|"
...

a bit verbose, but a possible starter.
awk -f bunny.awk inputfile2.txt inputfile1.fa where bunny.awk is:

function printRec() {
#print a[f], s[f], e[f]
for ( i in s) {
split(i,t,...

Try
awk '
$3 == "transcript" {match ($0, /cov[ ".0-9]*;/)
split (substr ($0, RSTART, RLENGTH), T, "\"")
PR = (T[2] > 3)
...

Well, looks like any tra_law line should reset the counters, regardless of the $5 - $4 delta value. Try this small adaption.



awk -F"\t" '
NR > 2 &&
$3 ~ /tra_law/ {if ((CNT > 3)...

Help me out: what does {NF--NF} do in your second awk script do? An uncommon construct, at least to me...

For your problem, how about
awk -F"\t" '
NR > 2 &&
($5-$4) > 200 &&
$3...

With a slight change it should also work nicely for string data values:

$ echo ' wrongkey "some data"; key "more data";' |
awk 'match($0, /[ ;]key +"[^"]*" *-;/)...

Try (untested)awk -F";" 'match ($0, /cov[ ".0-9]*;/) {split (substr ($0, RSTART, RLENGTH), T, "\""); if (T[2] <= 3) next} 1' file

Looks like you want to prefix every double quoted string with a space. How far would

sed 's/"[^"]*"/ &/g' file get you, provided the double quotes certainley, reliably appear in pairs?

$ sed -e 's/[^\t]*id/& \ /g' -e 's/[^\t]*alias_./& \ /g' file
Chr1 lnci exon 83801516 83803251 . - . gene_id "LINC01725"; transcript_id "LINC01725:44"; ...

Also note that I do not see any difference between your input and output examples. It is hard to help without an idea of what your tried. It also is extremely helpful for good answers to include...