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How to create a new file merging selective columns from two separate files using awk? Without messing up the elements orders of BOTH files.

Exemple: File 3 may contain column 1,2,3 from File 1 and column 4 from File 2.

File 1
A   23  8   T
A   63  9   9
B   45  3   J

File 2
A   0
A   6   
B   5

File 3
A   23  8   0
A   63  9   6
B   45  3   5
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up vote 2 down vote accepted

Try this:

$ awk 'FNR==NR{a[FNR]=$2;next};{$NF=a[FNR]};1' file2 file1
A 23 8 0
A 63 9 6
B 45 3 5
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Thanks! I also successfully tried this way out using gawk: pr -m -t -s\ File1.txt File2.txt | gawk '{print $1,$2,$3, $6}' > File3.txt – dovah Jul 21 '14 at 8:35
@Dovah: You can use paste file1 file2 and then print selected fields in awk. – cuonglm Jul 21 '14 at 8:50
This stores file2 in memory, which can be prohibitive if the files are large. There's a simpler way to do this without the memory overhead (see my answer). – Gilles Jul 21 '14 at 23:54

There's a dedicated tool for that: paste. It concatenates each full line from the first file with the corresponding line from the second file; you can remove unwanted columns before or after. For example, assuming that your columns are tab-delimited:

paste file1.txt file2.txt | cut -f 1,2,3,6

Here's a way to pre-filter both files that relies on ksh/bash/zsh process substitution.

paste <(<file1.txt sed 's/[[:space:]][[:space:]]*[^[:space:]]*$//') \
      <(<file1.txt sed 's/^[^[:space:]]*[[:space:]][[:space:]]*//')

Awk is primarily geared to processing one file at a time, but you can call getline to read from another file in parallel.

awk '
  BEGIN {file2=ARGV[2]; ARGV[2]="";}
  {$0 = $0 ORS getline(); print $1, $2, $3, $6;}
' file1.txt file2.txt

So far I've assumed that you want to match line 1 of file 1 with line 1 of file 2, line 2 of file 1 with line 2 of file 2, etc. If you want to match the contents of a column, that's a completely different matter. join will do the job provided that the column you want to match is sorted.

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