Here's a solution that combines/modifies both BrowserUk's and bobdabuilda's suggestions:

#!/usr/bin/perl
use warnings;
use strict;
use 5.010;

{    # Within this block because of the next line
    local $/ = undef;
    for(<DATA> =~ /(Data_Set.*?Count= 0)/gs) {

        my $counter = 0;
        my $total_aligned_reads = 0;
        my $mtDNA;

        for(split /\n/) {
            ## my $line = $_; #### Unnecessary; see next comment
            next if /(Data_Set_\d+: |^NoCoordinateCount|^$)/;
            ## next if /^NoCoordinateCount/;
            ## next if /^$/;
            my($chr, $lenLabel, $lengNumbers, $AlignedLabel, $alignedN
+umbers) = split /\s/; ####, $line; split operates on $_ by default
            $total_aligned_reads +=  $alignedNumbers;
            $mtDNA = $alignedNumbers if $chr eq "chrM";
        }

    say "total aligned reads = $total_aligned_reads";
    say "mtDNA = $mtDNA";
    say "mtDNA percentage = ", $mtDNA/$total_aligned_reads*100;
    }
}

__DATA__

[download]

Hope this helps!

In reply to Re: How to loop over multiple datasets (blocks of text)? by Kenosis
in thread How to loop over multiple datasets (blocks of text)? by rnaeye

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