in reply to counting the number of 16384 pattern matches in a large DNA sequence

@string = <IN1>;
chomp @string;

foreach my $string (@string) {
     foreach $key (keys %seq) {
        chomp $string;
         study $seq{$key};
       my @matches = ($seq{$key} =~ /$string/ig);
        #print "@matches\n";
        $result{$string} = scalar(@matches);
        }

foreach my $s (keys %result) {
        print "$s => $result{$s}\n";
        }

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Your current algorithm would be more efficient as: 

@string = <IN1>;
chomp @string;

while ( my $string = <IN1> ) {
    chomp $string;
    my ( $value ) = values %seq;
    my $result = () = $value =~ /$string/ig;

     print "$string => $result\n";
     }

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Replies are listed 'Best First'.
Re^2: counting the number of 16384 pattern matches in a large DNA sequence
by anonym (Acolyte) on Jun 14, 2012 at 20:47 UTC

    Hey, Thanks.I modified the code above as below to iterate over each value in the %seq hash and it works pretty fast :) 

    
while (my $string = <IN1>) {
        chomp $string;
        #my ($value) = values %seq;
        foreach $value (values %seq) {
        my $result = () = $value =~ /$string/g;
         print "$string => $result\n";
        }
}

    [download]
[reply]
[d/l]

      still for 16384 strings it is taking a lot of time to get the count.Hmm

[reply]

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