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Re: Improving the Nested For Loop

by BrowserUk (Patriarch)
on Sep 02, 2014 at 06:12 UTC ( [id://1099222]=note: print w/replies, xml ) Need Help??


in reply to Improving the Nested For Loop

You are doing an awful lot of completely unnecessary copying of arrays.

Try this clean-compiling (unlike your posted code), but untested version, It should be substantially faster:

#! perl -slw use strict; ## Variables and Data Structures my $count = 1; my @probesArray; my %probes; my $size = 100; ## Reading the file open my $FILE, "data.txt" or die "ERROR: cannot read file $!\n"; while (my $line = <$FILE>){ chomp $line; my @line = split '\t', $line; $probes{ $line[0] } = [ @line[ 1 .. $#line ] ]; ## value of the ha +sh as an array ## correlation between 1-2 or 2-1 will be same so using calculatin +g only once can be done thru this array $probesArray[ $count ] = $line[ 0 ]; $count++; } ## Frankly speaking reading of the file takes less than 3 sec with 50, +000 categories each having 100 values close $FILE; ## Correlation Calculation for( my $i = 0; $i <= $count-1; $i++ ){ for( my $j = $i+1; $j <= $count; $j++ ){ my $cor = correlation( $probes{ $probesArray[$i] }, $probes{ $ +probesArray[$j] }, $size ); ## correlation is the subroutine $probes{ $probesArray[$i] . "-" . $probesArray[$j] } = $cor; # print $count,"\t",$probesArray[$i]."-".$probesArray[$j],"\t",$ +cor,"\n"; $count++; } } ## Subroutines ## Pearson Correlation Coefficient sub correlation { my( $arr1, $arr2, $size ) = @_; my( $mean_x, $mean_y ) = mean( $arr1, $arr2, $size ); my( $ssxx, $ssxy, $ssyy ) = ss( $arr1, $arr2, $mean_x, $mean_y ); my $cor = $ssxy / sqrt( $ssxx * $ssyy ); return $cor ; } sub mean { my( $arr1, $arr2, $size ) = @_; my $mu_x = sum( @$arr1 ) / $size; my $mu_y = sum( @$arr2 ) / $size; return($mu_x,$mu_y); } ## Sum of Squared Deviations to the mean sub ss { my( $arr1, $arr2, $mean_x, $mean_y ) = @_; my( $ssxx, $ssxy, $ssyy ) = (0) x 3; ## looping over all the samples for( my $i = 0; $i < @$arr1; $i++ ){ $ssxx = $ssxx + ( $arr1->[$i] - $mean_x )**2; $ssxy = $ssxy + ( $arr1->[$i] - $mean_x ) * ( $arr2->[$i] - $m +ean_y ); $ssyy = $ssyy + ( $arr2->[$i] - $mean_y )**2; } return ($ssxx, $ssxy, $ssyy); }

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