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@thearray = (1, 4, 6)
my $line = <INFILE>;
...
foreach(my $i = 0; $i <= $#thearray; $i++)   {
  push @bigarray[$thearray[$i]], [$line, $column[$thearray[$i]];
}

@array_1 = [$line, $column[1]]
@array_4 = [$line, $column[4]]
@array_6 = [$line, $column[6]]