Syntax error on file name when using awk to compare two files

Question

I'm trying to use awk to print the lines contained in one file2 if the numbers in column 1 or 5 is in file1, but I'm getting a syntax error that I don't understand.

My input is:

file1.dat

1
3
4
6
8
13
14
25

etc...

file2.dat

2 GLU 1 - 3 ARG 2
24 ASP 2 - 12 LYS 1
3 ASP 1 - 25 ARG 2
7 LYS 2 - 17 GLU 2
18 ARG 1 - 13 GLU 2

etc...

In this case I want the output

2 GLU 1 - 3 ARG 2
3 ASP 1 - 25 ARG 2
18 ARG 1 - 13 GLU 2

I tried to do this with the following awk-line

awk -F 'NR==FNR{a[$1||$5]++;next} (a[$1||$5])' file1.dat file2.dat

but I get the error

awk: file1.dat
awk:      ^syntax error

Does anyone know what is causing this error? I have tried to put the file names into variables but that produces the same error.

I am not sure how the script (or algorithm) would work, but the syntax error is due to treating "file1.dat" as awk code, because the actual awk code got treated as the "input field separator" by -F. If you remove that -F, this specific syntax error may go away, but not sure if you will get the required output. — Prem
– Prem, Commented May 9, 2015 at 18:36

ShellFish · Accepted Answer · 2015-05-09 18:01:36Z

4

You have supplied the -F flag for field separator. The next argument is therefore the fields separator (which is your script because you didn't supply a seperator). So awk takes the first file as the script itself.

Try to either drop the -F or adding a separator e.g. awk -F '[ \t]*' '...' file1 file2.

answered May 9, 2015 at 18:01

ShellFish

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