Monks,

I have an efficiency question. I need to create a super large tab delimited file. 4^7 by 4^7 in dimension. What I have now is a double loop which prints out each element individually in its appropriate location. This file is a symmetric square matrix. I am unsure whether it will take more time to save 0.5 *4^7 *4^7 entries to RAM so that I only calculate once, or whether it would be better to calculate each element twice inside the double loop. If any of the monks are especially bored, I would also appreciate comments on how I could improve the efficiency of the code below. Please forgive me if there are glaring errors, I am not a programmer, just a lowly grad student pretending to be one.

#!/usr/bin/perl
use strict;
use warnings;

my @kmers=<>;
chomp @kmers;
my $kmer_l=length($kmers[0]);
for(my $j=0;$j<@kmers;++$j){
    print &map_constraint($kmer_l,&return_constraint($kmers[$j],$kmers
+[0]));
    for(my $i=1;$i<@kmers;++$i){
        print "\t",&map_constraint($kmer_l,&return_constraint($kmers[$
+j],$kmers[$i]));
    }
    print "\n";
}

sub map_constraint{
    my $dt=0.0000000001;
##input string length,and edit distance value
    return (-(($_[1]+$dt)/(($_[0]/2)+$dt)-1)) ##returns a value from (
+-1,1) 
}

sub return_constraint{#string edit distance
    my ($len1, $len2) = (length $_[0], length $_[1]);
    if ($len1 == 0){
        return $len2;
    }
    if ($len2 == 0){
        return $len1;
    }
    my %hash;
    for(my $i=0;$i<=$len1;++$i){
        for(my $j=0;$j<=$len2;++$j){
            $hash{$i}{$j} = 0;
            $hash{0}{$j} = $j;
        }
        $hash{$i}{0}=$i;
    }
    my @a=split(//, $_[0]);
    my @b=split(//, $_[1]);
    for(my $i=1;$i<=$len1;++$i){
        for (my $j=1;$j<=$len2;++$j){
            my $cost=($a[$i-1] eq $b[$j-1]) ? 0 : 1;
            $hash{$i}{$j}=&min([$hash{$i-1}{$j} + 1,$hash{$i}{$j-1} + 
+1,$hash{$i-1}{$j-1} + $cost]);
        }
    }
    return $hash{$len1}{$len2};
}

sub min{
    my $min=${$_[0]}[0];
    foreach my $elem (@{$_[0]}){
        if($elem < $min){
            $min=$elem;
        }
    }
    return $min;

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In reply to Efficiency of implementation by azheid

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