Use lexical file handles, three parameter open and test the result of open:

open my $log, '>', $logfile or die "Failed to create $logfile: $!\n";

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Hashes and arrays are born empty so there is no need to explicitly flush them with my %hits = (); (for example). A simple my %hits; gets the job done and results in less clutter.

Use Perl loops. They are easier to understand and are less error prone than C style for loops. Instead of:

for (my $round = 1; $round <= $roundlimit; $round++) {

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use:

for my $round (1 .. $roundlimit) {

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and instead of monkeying around with the loop counter to exit the loop simply use last:

        if ($hitcount == 0) {
            print $log "Hitcount: $hitcount through Round $round ==> S
+TOP\n";
            last;
        }

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Don't worry about the files getting closed. The lexical file handles going out of scope will take care of that for you.

True laziness is hard work

In reply to Re: Iterative BLAST(N) program by GrandFather
in thread Iterative BLAST(N) program by Tjuh

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