You haven't specified how the lines from the two files should match. I've presumed the first two columns should be the same: 
my @file_one = (
    '1   100   5730_1 0.123',
    '1   200   5730_1 4.567',
    '21  400   5785_3 2.345',
);

my @file_two = (
    '1   100   1',
    '1   200   1',
    '21  400   60',
);

my %file2;
for my $line ( @file_two ) {
    my @f = split /\s+/, $line;
    $file2{$f[0]}{$f[1]} = $f[2];
}

for my $line ( @file_one ) {
    my @f = split /\s+/, $line;
    die "can't find match for $line"
      unless exists $file2{$f[0]}{$f[1]};

    print "$f[0] $f[1] $file2{$f[0]}{$f[1]} $f[3]\n";
}

[download]

Output: 

1 100 1 0.123
1 200 1 4.567
21 400 60 2.345

[download]

In reply to Re: merge files by column (revisted) by FunkyMonk
in thread merge files by column (revisted) by j1n3l0

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.