awk match and find mismatch between files and output results - awk

Question

In the below awk I am using $5 $7 and $8 of file1 to search $3 $5 and $6 of file2. The header row is skipped and it then outputs a new file with what lines match and if they do not match what file the match is missing from. When I search for one match use 3 fields for the key for the lookup and do not skip the header I get current output. I apologize for the long post and file examples, just trying to include everything to help get this working. Thank you :).
file1
Index Chromosomal Position Gene Inheritance Start End Ref Alt Func.refGene
98 48719928 FBN1 AD 48719928 48719929 AT - exonic
101 48807637 FBN1 AD 48807637 48807637 C T exonic
file2
R_Index Chr Start End Ref Alt Func.IDP.refGene
36 chr15 48719928 48719929 AT - exonic
37 chr15 48719928 48719928 A G exonic
38 chr15 48807637 48807637 C T exonic
awk
awk -F'\t' '
NR == FNR {
A[$25]; A[$26]; A[$27]
next
}
{
B[$3]; B[$5]; B[$6]
}
END {
print "Match"
OFS=","
for ( k in A )
{
if ( k && k in B )
printf "%s ", k
}
print "Missing from file1"
OFS=","
for ( k in B )
{
if ( ! ( k in A ) )
printf "%s ", k
}
print "Missing from file2"
OFS=","
for ( k in A )
{
if ( ! ( k in B ) )
printf "%s ", k
}
}
' file1 file2 > list
current output
Match
Missing from file1
A C Ref 48807637 Alt Start T G - AT 48719928 Missing from file2
desired output
Match 48719928 AT -, 48807637 C T
Missing from file1 48719928 A G
Missing from file2

Answer 1

You misunderstand awk syntax and are confusing awk with shell. When you wrote:
A[$25] [$26] [$27]
you probably meant:
A[$25]; A[$26]; A[$27]
(and similarly for B[]) and when you wrote:
IFS=
since IFS is a shell variable, not an awk one, you maybe meant
FS=
BUT since you're doing that in the END section and not calling split() and so not doing anything that would use FS idk what you were hoping to achieve with that. Maybe you meant:
OFS=
BUT you aren't doing anything that would use OFS and your desired output isn't comma-separated so idk what you'd be hoping to achieve with that either.
If that's not enough info for you to solve your problem yourself then reduce your example to something with 10 columns or less so we don't have to read a lot of irrelevant info to help you.

Answer 2

Program 1
This works, except the output format is different from what you request:
awk 'FNR==1 { next }
FNR == NR { file1[$5,$7,$8] = $5 " " $7 " " $8 }
FNR != NR { file2[$3,$5,$6] = $3 " " $5 " " $6 }
END { print "Match:"; for (k in file1) if (k in file2) print file1[k] # Or file2[k]
print "Missing in file1:"; for (k in file2) if (!(k in file1)) print file2[k]
print "Missing in file2:"; for (k in file1) if (!(k in file2)) print file1[k]
}' file1 file2
Output 1
Match:
48807637 C T
48719928 AT -
Missing in file1:
48719928 A G
Missing in file2:
Program 2
If you must have each set of values in a category comma-separated on a single line, then:
awk 'FNR==1 { next }
FNR == NR { file1[$5,$7,$8] = $5 " " $7 " " $8 }
FNR != NR { file2[$3,$5,$6] = $3 " " $5 " " $6 }
END {
printf "Match"
pad = " "
for (k in file1)
{
if (k in file2)
{
printf "%s%s", pad, file1[k]
pad = ", "
}
}
print ""
printf "Missing in file1"
pad = " "
for (k in file2)
{
if (!(k in file1))
{
printf "%s%s", pad, file2[k]
pad = ", "
}
}
print ""
printf "Missing in file2"
pad = " "
for (k in file1)
{
if (!(k in file2))
{
printf "%s%s", pad, file1[k]
pad = ", "
}
}
print ""
}' file1 file2
The code is a little bigger, but the format used exacerbates the difference. The change is all in the END block; the other code is unchanged. The sequences of actions in the END block no longer fit comfortably on a single line, so they're spread out for readability. You can apply a liberal smattering of semicolons and concatenate the lines to shrink the apparent size of the program if you desire.
It's tempting to try a function for the printing, but the conditions just make it too tricky to be worthwhile, I think — but I'm open to persuasion otherwise.
Output 2
Match 48807637 C T, 48719928 AT -
Missing in file1 48719928 A G
Missing in file2
This output will be a lot harder to parse than the one shown first, so doing anything automatically with it will be tricky. While there are only 3 entries to worry about, the line length isn't an issue. If you get to 3 million entries, the lines become very long and unmanageable.