BrowserUk:

Ah, well, I know jack about FASTA files, so I didn't consider that. Of course, by changing the reader to accumulate records instead of lines, it could be adapted. Though since there are already a couple working examples from you and Marshall, and since mine has a bias in it, there's no real reason to do so.

I know that *you* know how to do the changes, but if someone tripping across this node in the future wants to do it, you can do so something (untested!) like this:

my @record;
while (<$FH>) {
    if (/start of record marker/) {
        ++$cnt_recs;
        if ($num/$cnt_recs > rand) {
            my $i=@samples;
            if ($i > $num) { $i = rand @samples; }
            $samples[$i]=[$cnt_recs, [@record]];
        }
    }
    else {
        # Accumulate record
        push @record, $_;
    }
}
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...roboticus

When your only tool is a hammer, all problems look like your thumb.