match 1,2,5 columns of file1 with 1,2,3 columns of file2 respectively and output should have matched rows from file 2. second file is zipped file .gz

Question

file1

3   1234581 A   C   rs123456

file2 zipped file .gz

1   1256781 rs987656    T   C
3   1234581 rs123456    A   C
22  1792471 rs928376    G   T

output

3   1234581 rs123456    A   C

I tried

zcat file2.gz | awk 'NR==FNR{a[$1,$2,$5]++;next} a[$1,$2,$3]' file1.txt  - > output.txt

but it is not working

Did you try anything at all? It's customary to show some trials, good or bad. — James Brown, Jul 12 '21 at 09:41

RavinderSingh13 · Accepted Answer · 2021-07-12T09:59:06.170

2

Please try following awk code for your shown samples. Use zcat to read your .gz file and then pass it as 2nd input to awk program for reading, after its done reading with file1.

zcat your_file.gz | awk 'FNR==NR{arr[$1,$2,$5];next} (($1,$2,$3) in arr)' file1 -

Fixes in OP's attempt:

You need not to increment value of array while creating it in file1. Just existence of indexes in it will be enough.
While checking condition in reading file2(passed by zcat command) just check if respective fields are present in array if yes then print that line.

edited Jul 12 '21 at 09:59

answered Jul 12 '21 at 09:53

RavinderSingh13

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I need to match columns 1,2,5 of file1 together to column 1,2,3 of second zipped file – rij Jul 12 '21 at 09:57
@rij, yes please check my updated answer(refresh this page) I have updated my answer, let me know. – RavinderSingh13 Jul 12 '21 at 09:57
'FNR==NR{arr[$1,$2,$5];next} ($1,$2,$3 in arr)' wont work right ? – rij Jul 12 '21 at 09:58
@rij, I have tested it and it worked fine for me with your shown samples. use file2 with zcat command and pass file1 as input file to `awk` program. – RavinderSingh13 Jul 12 '21 at 09:59

match 1,2,5 columns of file1 with 1,2,3 columns of file2 respectively and output should have matched rows from file 2. second file is zipped file .gz

1 Answers1