awk to match file1 and extract specific tag values
File2 is tab-delimeted and I am trying to use $2 in file1 (space delimeted) as a search term in file2. If it is found then the AF= in and the FDP= values from file2 are extracted and printed next to the file1 line. I commented the awk before I added the lines in bold the current output resulted. I also can not figure out how to change the FDP= to READS=. Thank you .
Code:
script.awk
BEGIN { OFS="\t" }
# Read $2 search terms from file1 into 's'
FNR==NR {
s[$2]
next
}
{ match($8,/'"'"'normalizedPos'"'"':'"'"'/, pos) # extract and read into pos value after :
}
{ match($8,/(AF=[^;]+).*(FDP=[^;]+)/, info) # extract and read into info value after AF= and FDP=
print $1":"pos[1],gene[1],info[2],info[1] ($1 in s ? s[$1] : "NOT DETECTED") # print desired output
}
awk -f script.awk file FS='\t' file2
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04567,04567.xml
12134,12134.xml
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01-02-2019
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