ID5144.C2039 
ID5141.C2039
ID5142.C1221

my ($first, $second) = map {s/.*\.//; $_} split ' ';

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Are you deleting the first half of the ID?
While the first column contains only "ID5141"'s the second column does contain unique prefixes that are probably important to the problem.

ID5144.C2039 is different from ID5141.C2039, for example.

In reply to Re^2: clustering pairs by SuicideJunkie
in thread clustering pairs by sugar

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