You are basically just manually doing a SQL JOIN in the code -- you can simplify this by letting the database (in this case i see it's postgres) do the work:
... # open file; connect to $dbh
my $sth = $dbh->prepare(qq{
SELECT
d1.d_id as did1,
d2.d_id as did2,
d1.c_id as cid1,
d2.c_id as cid2
FROM d as d1, d as d2
WHERE d1.d_id = ?
AND d2.d_id = ?
AND d1.c_id != d2.c_id
});
while(<INPUT>){
my( $did1, $did2, $score1, $score2 ) = split "\t", $_;
next unless $score1 >=70 && $score2 >=60;
$sth->execute($did1,$did2);
while( my $row = $sth->fetchrow_arrayref ){
print join(', ', @$row), "\n";
}
}
close INPUT;
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