nested awk commands? - awk

Question

I have got following two codes:
nut=`awk "/$1/{getline; print}" ids_lengths.txt`
and
grep -v '#' neco.txt |
grep -v 'seq-name' |
grep -E '(\S+\s+){13}\bAC(.)+CA\b' |
awk '$6 >= 49 { print }' |
awk '$6 <= 180 { print }' |
awk '$4 > 1 { print }' |
awk '$5 < $nut { print }' |
wc -l
I would like my script to replace "nut" at this place:
awk '$4 < $nut { print }'
with the number returned from this:
nut=`awk "/$1/{getline; print}" ids_lengths.txt`
However, $1 in code just above should represent not column from ids_lengths.txt, but first column from neco.txt! (similiarly as I use $6 and $4 in main code).
A help how to solve these nested awks will definitely be appreciated:-)
edit:
Line of my input file (neco.txt) looks like this:
FZWTUY402JKYFZ 2 100.000 3 11 9 4.500 7 0 0 0 . TG TGTGTGTGT
The biggest problem is that I want to filter those lines that have in the fifth column number less than number, which I get from another file (ids_lengths.txt), when searching with first column (e.g. FZWTUY402JKYFZ). That's why I put "nut" variable in my draft script :-)
ids_lengths.txt looks like this:
>FZWTUY402JKYFZ
153
>FZWTUY402JXI9S
42
>FZWTUY402JMZO4
158

Answer 1

You can combine the two grep -v operations and the four consecutive awk operations into one of each. This gives you useful economy without completely rewriting everything:
nut=`awk "/$1/{getline; print}" ids_lengths.txt`
grep -E -v '#|seq-name' neco.txt |
grep -E '(\S+\s+){13}\bAC(.)+CA\b' |
awk -vnut="$nut" '$6 >= 49 && $6 <= 180 && $4 > 1 && $5 < nut { print }' |
wc -l
I would not bother to make a single awk script determine the value of nut and do the value-based filtering. It can be done, but it complicates things unnecessarily — unless you can demonstrate that the whole thing is a bottleneck for the performance of the production system, in which case you do work harder (though I'd probably use Perl in that case; it can do the whole lot in one command).

Answer 2

Approximately:
awk -v select="$1" '$0 ~ select && FNR == NR { getline; nut = $0; } FNR == NR {next} $4 > 1 $5 < nut && $6 >= 49 && $6 <= 180 && ! /#/ && ! /seq-name/ && $NF ~ /^AC.+CA$/ {count++} END {print count}' neco.txt ids_lengths.txt
The regex will need to be adjusted to something that AWK understands. I can't see how the regex matches the sample data you provided. Part of the solution may be to use a field count as one of the conditions. Perhaps NF == 13 or NF >= 13.
Here's the script above broken out on multiple lines for readability:
awk -v select="$1" '
$0 ~ select && FNR == NR {
getline
nut = $0;
}
FNR == NR {next}
$4 > 1
$5 < nut &&
$6 >= 49 &&
$6 <= 180 &&
! /#/ &&
! /seq-name/ &&
$NF ~ /^AC.+CA$/ {
count++
}
END {
print count
}' ids_lengths.txt neco.txt