Join two files using awk

Question

I have two files like shown below which are tab-delimited:

file A

chr1   123 aa b c d
chr1   234 a  b c d
chr1   345 aa b c d
chr1   456 a  b c d
...         


        

Answer 1

You can use join, but the pipeline gets so complicated it might be easier to switch to a more powerful language like Perl.

join -11 -21 -o1.1,1.2,1.3,1.4,1.5,2.4,2.5 \
     <(sed 's/ \+/:/' fileA | sort) \
     <(sed 's/ \+/:/' fileB | sort) \
 | join -11 -22 -a1 -o1.1,1.2,1.3,1.4,1.5,1.6,1.7,2.5,2.6 \
     - <(sed 's/ \+\([^ ]\+\) \+\([^ ]\+\)/ \1:\2/' fileC | sort -k2) \
 | sed 's/:/ /'

Perl solution, using a hash to remember all the information:

#!/usr/bin/perl
use warnings;
use strict;

#             key_start  key_end  keep_from  output
my %files = (A => [0,      1,      2,       [0 .. 3]],
             B => [0,      1,      2,       [-2, -1]],
             C => [1,      2,      3,       [-2, -1]],
            );

my %hash;

for my $file (keys %files) {
    open my $FH, '<', "file$file" or die "file$file: $!";
    while (<$FH>) {
        my @fields = split;
        $hash{"@fields[$files{$file}[0], $files{$file}[1]]"}{$file}
            = [ @fields[$files{$file}[2] .. $#fields] ];
    }
}

for my $key (sort keys %hash) {
    print $key, join(' ', q(),
                     grep defined, map {
                         @{ $hash{$key}{$_} }[@{ $files{$_}[-1] }]
                     } sort keys %files), "\n";
}