If I understand you right, you need to count each pairwise combination in a hash.

To avoid confusion between the combinations ("A","B") and ("B","A") you need to "normalize" i.e. in this case to sort the key "vector" into a unique "representative" (here ("A","B")).

Now you can either use a HoH $h{A}{B}++ or use this old multi-dim feature from Perl4 by separting keys by comma $h{A,B}++!

I prefer the latter.

Code example to follow...¹

UPDATE: IIRC comma as separator is more secure than using an arbitrary separator like "_" but since I can't find the docs for multi dim keys and² your input already uses space as separator, you should stick with it. I.e. changing the code below to $count{"@keys[$a,$b]"}++

{
  "aesG gly4" => 2,
  "aesG phil" => 2,
  "aesG tomD" => 2,
  "gly4 phil" => 2,
  "gly4 tomD" => 3,
  "phil tomD" => 2,
}

[download]

Cheers Rolf

1) 

use Data::Dump "pp";
my %count;
 
 
while(<DATA>) {
  chomp;
  @keys= sort split;
  for my $a (0..$#keys){
    for my $b ($a+1.. $#keys) {
#     pp [$keys[$a],$keys[$b]];
      $count{$keys[$a],$keys[$b]}++
    }
  }
  
}
 
pp \%count;
 
__DATA__
tomD gly4 phil
aesG tomD gly4 phil
aesG phil
aesG tomD gly4

[download]

prints

{
  "aesG\34gly4" => 2,
  "aesG\34phil" => 2,
  "aesG\34tomD" => 2,
  "gly4\34phil" => 2,
  "gly4\34tomD" => 3,
  "phil\34tomD" => 2,
}

[download]

2) see $;

In reply to Re: counting pairwise incidences by LanX
in thread counting pairwise incidences by reubs85

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.