Re^2: write hash to disk after memory limit

[hailholyghost]

thanks a lot, I've been using hash-hash-array-array in order to keep memory use down. I think array access is also faster than hash, so I did this:

foreach my $rat (@directories) {
      print "Reading Merged_99$rat/bs_seeker-CG.tab ...\n";
      open(FH,"<Merged_99$rat/bs_seeker-CG.tab") or die "cannot read M
+erged_99$rat/bs_seeker-CG.tab: $!";
      while (<FH>) {
         if (/M/) {
            next;
         } elsif ((/^chr(\S+)\s+(\d+)\s+\d+\s+(\d)\.(\d+)\s+(\d+)/) &&
+ ($1 ~~ @CHROMOSOMES) && ($5 >= $MINIMUM_COVERAGE)) {
#chromosome $1, methylated C $2, percent $3.$4 and coverage $5
            $DATA{$1}{$2}[$set][$replicate] = "$3.$4";
         } elsif ((/^chr(\S+)\s+(\d+)\s+\d+\s+(\d)\s+(\d+)/) && ($1 ~~
+ @CHROMOSOMES) && ($4 >= $MINIMUM_COVERAGE)) {
            $DATA{$1}{$2}[$set][$replicate] = $3;
         }
      }
      close FH;
      $replicate++;
   }

[LanX]

As I said, better

> > organize the upper tier roughly according to the timeline of your process

No idea where $set comes from but $replicate could be such a top tier.

so $data[$set][$replicate]{$1}{$2} should have far less memory swapping problems (AFAIS).

(BTW better reserve uppercase var-names to perl buit-ins)

If this structure doesn't fit into your future plans, you most likely want to use a DB anyway.

[Jenda]

Do you later use the value as a string or as a number? If you use it as a number, I believe you could save quite a bit of memory by forcing a conversion before storing the data. The way you do it, you end up with a scalar containing both the string and (as soon as you use the number for the first time) the number.

...
$DATA{$1}{$2}[$set][$replicate] = 0 + "$3.$4";
         } elsif ((/^chr(\S+)\s+(\d+)\s+\d+\s+(\d)\s+(\d+)/) && ($1 ~~
+ @CHROMOSOMES) && ($
+4 >= $MINIMUM_COVERAGE)) {
            $DATA{$1}{$2}[$set][$replicate] = 0 + $3;
...