I can't tell because I don't know what the lines you are dealing with look like. I can only help with overall structure and technique. On the face of it the handling looks OK, but it does depend very much on the content of the first two fields on each line. Can the letter case of the contents be different or can numeric representation be different between the fields for example?

I've applied the changes I suggested in my reply along with a few others to give:

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

sub iterblast {
    # settings
    my $myblast = "blastall -p blastn -m 8";
    my $starterseq =
        "/share/home/tjuh/Thema12-2011/Project/testblast/matchedhits.f
+asta";
    my $blastdb =
        "/share/home/tjuh/Thema12-2011/Project/databases/termite_hindg
+ut/hindgut_db";
    my $outputroot = "/share/home/tjuh/Thema12-2011/Project/testblast/
+test1";
    my $evalue     = 0.01;
    my $wordsize   = 11;
    my $roundlimit = 4;

    # output files:
    my $seq_db_fasta = $outputroot . ".tmp";
    my $seq_db_all   = $outputroot . ".all";
    my $logfile      = $outputroot . ".log";

    # remove existing files
    unlink $seq_db_fasta;
    unlink $seq_db_all;
    unlink $logfile;

    open my $log, '>', $logfile or die "Can't open $logfile: $!\n";
    print $log <<LOGMSG;
Configurations:
Input file       : $starterseq
Output files     : $outputroot\-
Blast Engine     : $myblast
Target database  : $blastdb
E-value cut-off  : $evalue
Blast word size  : $wordsize
Blast round limit: $roundlimit

Runs:
LOGMSG

    # hits hash
    my %hits;
    my %queryids;

    # Start the iterative blastn rounds
    for my $round (1 .. $roundlimit) {
        my $saveblst = $outputroot . ".txt";
        
        unlink $saveblst;

        # print $log info
        my $curtime = localtime();
        my $infile = $round == 1 ? $starterseq : $seq_db_fasta;

        print $log "$curtime - Blast seq: $infile\n";
        print $log "$curtime - Blast db : $blastdb\n";

        # run blast
        system(
            "$myblast -i $infile -d $blastdb -o $saveblst -e $evalue -
+W $wordsize"
            );

        open my $parse, '<', $saveblst or die "Can't open $saveblst: $
+!\n";
        open my $fasta, '>', $seq_db_fasta
            or die "Can't create $seq_db_fasta: $!\n";

        # parse blast output (tab form) and add matched id's in hits h
+ash
        while (defined (my $line = <$parse>)) {
            chomp $line;
            my @fields = split(/\t/, $line);
            ++$queryids{$fields[0]};
            ++$hits{$fields[1]};
        }

        # get header and sequence with 'fastacmd' and write to new fas
+ta file
        my $hitcount;

        while (my $key = each %hits) {
            next if exists $queryids{$key};

            # only write uniq ids to file
            system("fastacmd -d $blastdb -s 'lcl|$key' >> $seq_db_fast
+a");
            $hitcount++;
        }

        close $fasta;
        close $parse;

        if ($hitcount) {
            print $log "Round $round has $hitcount unique hits\n\n";
            next;
        }

        print $log "No hits in Round $round ==> STOP\n";
        last;
    }

    print "Total uniq hits found in all rounds: ", scalar keys %hits, 
+"\n";
    close($log);
}
[download]

Note that I've eliminated system calls to delete files and get the date and replaced them with the equivalent Perl functions! So far as I can see there are no changes in the logic of the code, but to my mind it is somewhat cleaner.

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.