Match specific pattern and print just the matched string in the previous line - awk

Question

I update the question with additional information
I have a .fastq file formatted in the following way
#M01790:39:000000000-C3C6P:1:1101:14141:1618 1:N:0:8 (sequence name)
CATCTACATATTCACATATAGACATGAAACACCTGTGGTTCTTCCTC.. (sequence)
+
ACCCGGGGGGGGGDGGGFGGGGGGFGGGGGGGGGGGFGGGGFGFGFF.. (sequence quality)
For each sequence the format is the same (repetition of 4 lines)
What I am trying to do is searching for a specific regex pattern ([A-Z]{5,}ACA[A-Z]{5,}ACA[A-Z]{5,})in a window of n=35 characters of the 2nd line, cut it if found and report it at the end of the previous line.
So far I've written a bunch of code that does almost what I want.I thought using the match function together wit the substr of my window of interest but i didn't achieve my goal. I report below the script.awk :
match(substr($0,0,35),/regexp/,a) {
print p,a[0] #print the previous line respect to the matched one
print #print the current line
for(i=0;i<=1;i++) { # print the 2 lines following
getline
print
}
}#store previous line
{ p = $0 }
Starting from a file like this:
#M01790:39:000000000-C3C6P:1:1101:14141:1618 1:N:0:8
AACATCTACATATTCACATATAGACATGAAACACCTGTGGTTCTTCCTC..
+
GGGGGGGGDGGGFGGGGGGFGGGGGGGGGGGFGGGGFGFGFFGGGGFGF..
I would like to obtain an output like this:
#M01790:39:000000000-C3C6P:1:1101:14141:1618 1:N:0:8 TATTCACATATAGACATGAAA #is the string that matched the regexp WITHOUT initial AA that doesn' match my expression
ATATTCACATATAGACATGAAACACCTGTGGTTCTTCCTC #without initial AA
+
GGGFGGGGGGFGGGGGGGGGGGFGGGGFGFGFFGGGGFGF # without "GGGGGGGGDGGGFGGGGGGFGGG" that is the same number of characters removed in the 2nd line

Answer 1

$ cat tst.awk
BEGIN {
tgtStr = "pattern"
tgtLgth = length(tgtStr)
winLgth = 35
numLines = 4
}
{
lineNr = ( (NR-1) % numLines ) + 1
rec[lineNr] = $0
}
lineNr == numLines {
if ( idx = index(substr(rec[2],1,winLgth),tgtStr) ) {
rec[1] = rec[1] " " tgtStr
rec[2] = substr(rec[2],idx+tgtLgth)
rec[4] = substr(rec[4],idx+tgtLgth)
}
for ( lineNr=1; lineNr<=numLines; lineNr++ ) {
print rec[lineNr]
}
}
$ awk -f tst.awk file
#M01790:39:000000000-C3C6P:1:1101:14141:1618 1:N:0:8 pattern
ATATTCACATATAGACATGAAACACCTGTGGTTCTTCCTC..
+
GGGFGGGGGGFGGGGGGGGGGGFGGGGFGFGFFGGGGFGF..
wrt the code you posted:
substr($0,0,35) - strings, fields, line numbers, and arrays in awk start at 1 not 0 so that should be substr($0,1,35). Awk will compensate for your mistake and treat it as if you had written 1 instead of 0 in this case but get used to starting everything at 1 to avoid mistakes when it matters.
for(i=0;i<=1;i++) - should be for(i=1;i<=2;i++) for the same reason.
getline - not an appropriate use and syntactically fragile, see for(i=0;i<=1;i++)
Update - per your comment below that pattern is actually a regexp rather than a string:
$ cat tst.awk
BEGIN {
tgtRegexp = "[A-Z]{5,}ACA[A-Z]{5,}ACA[A-Z]{5,}"
winLgth = 35
numLines = 4
}
{
lineNr = ( (NR-1) % numLines ) + 1
rec[lineNr] = $0
}
lineNr == numLines {
if ( match(substr(rec[2],1,winLgth),tgtRegexp) ) {
rec[1] = rec[1] " " substr(rec[2],RSTART,RLENGTH)
rec[2] = substr(rec[2],RSTART+RLENGTH)
rec[4] = substr(rec[4],RSTART+RLENGTH)
}
for ( lineNr=1; lineNr<=numLines; lineNr++ ) {
print rec[lineNr]
}
}

Answer 2

I warn you, I wanted to have some fun and it is twisted.
awk -v pattern=pattern -v window=15 '
BEGIN{RS="#";FS=OFS="\n"}
{pos = match($2, pattern); n_del=pos+length(pattern)}
pos && (n_del<=window){$1 = $1 " " pattern; $2=substr($2, n_del); $4=substr($4, n_del)}
NR!=1{printf "%s%s", RS, $0}
' file
Input :
#M01790:39:000000000-C3C6P:1:1101:14141:1618 1:N:0:8
CATCTACpatternATATTCACATATAGACATGAAACACCTGTGGTTCTTCCTC..
+
ACCCGGGGGGGGGDGGGFGGGGGGFGGGGGGGGGGGFGGGGFGFGFFGGGGFGF..
#M01790:39:000000000-C3C6P:1:1101:14141:1618 1:N:0:8
CATCTACGCpatternATATTCACATATAGACATGAAACACCTGTGGTTCTTCCTC..
+
ACCCGGGGDGGGGGGDGGGFGGGGGGFGGGGGGGGGGGFGGGGFGFGFFGGGGFGF..
Output :
#M01790:39:000000000-C3C6P:1:1101:14141:1618 1:N:0:8 pattern
ATATTCACATATAGACATGAAACACCTGTGGTTCTTCCTC..
+
GGGFGGGGGGFGGGGGGGGGGGFGGGGFGFGFFGGGGFGF..
#M01790:39:000000000-C3C6P:1:1101:14141:1618 1:N:0:8
CATCTACGCpatternATATTCACATATAGACATGAAACACCTGTGGTTCTTCCTC..
+
ACCCGGGGDGGGGGGDGGGFGGGGGGFGGGGGGGGGGGFGGGGFGFGFFGGGGFGF..
Second block is not updated because window is 15 and it cannot find the pattern within this window.
I used variable RS to deal with entire 4 lines block with $0, $1, $2, $3 and $4. Because input file starts with RS and does not end with RS, I prefered to not set ORS and use printf instead of print.