awk search column from one file, if match print columns from both files

Question

I\'m trying to compare column 1 from file1 and column 3 from file 2, if they match then print the first column from file1 and the two first columns from file2.

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Answer 1

You can use this awk:

awk -F '[| ]+' -v OFS='\t' 'NR==FNR{a[$4]=$1 OFS $2; next}
       $1 in a{print $1, a[$1]}' file2 file1
Cre01.g000100   chromosome_1    99034
Cre01.g000500   chromosome_1    71569
Cre01.g000650   chromosome_1    93952

Answer 2

Your middle attempt of the three is closest, but:

• You haven't specified the field delimiter is |.
• You don't assign to a[$1].

• Your sample output is inconsistent with your desired output (the sample output shows column 1 from file 1 and column 1 from file 2; the desired output is reputedly column 1 from file 1 and columns 1 and 2 from file 2, though this interpretation depends on the interpretation of $3 in file 2 being the name between two pipe symbols).

  Citing the question at the time this answer was created:

  … compare column 1 from file1 and column 3 from file 2, if they match then print the first column from file1 and the two first columns from file2.

  desired output
  Cre01.g000100  chromosome_1    99034
  Cre01.g000500  chromosome_1    71569
  Cre01.g000650  chromosome_1    93952
  

• We can observe that if $3 in file 2 is equal to a value from file 1, then it is as easy to print $3 as a saved value.

So, fixing this up:

awk -F'|' 'NR==FNR { a[$1]=1; next } ($3 in a) { print $3, $1 }' file1 file2

The key change is the assignment to a[$1] (and the -F'|'); the rest is cosmetic and can be tweaked to suit your requirements (since the question is self-inconsistent, it is hard to give a better answer).