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

my @roundData = (<<DATA1, <<DATA2);
2004112448	2004112448	100.00	738	0	0	1	738	1	738	0.0	1421
2004112448	2004113832	90.44	586	54	2	153	738	16	599	0.0	 660
2004112448	2004101124	89.67	368	37	1	361	728	1	367	3e-104	 379
2004112448	2004105206	83.33	606	101	0	76	681	4	609	1e-100	 367
2004112448	2004086271	85.95	363	51	0	341	703	83	445	5e-75	 281
2004112448	2004120286	80.98	205	39	0	208	412	373	577	1e-19	97.6
2004112448	2004133966	91.43	70	6	0	618	687	261	192	9e-18	91.7
2004112448	2004136134	87.84	74	9	0	193	266	345	418	5e-13	75.8
2004112448	2004112239	84.34	83	13	0	461	543	101	183	8e-09	61.9
2004112448	2004112239	89.36	47	5	0	366	412	6	52	2e-06	54.0
2004112448	2004097170	85.14	74	11	0	193	266	346	419	3e-08	60.0
2004112448	2004127588	86.15	65	9	0	193	257	346	410	1e-07	58.0
2004112448	2004119982	86.15	65	9	0	193	257	346	410	1e-07	58.0
2004112448	2004100435	86.15	65	9	0	193	257	55	119	1e-07	58.0
2004112448	2004135256	82.56	86	15	0	184	269	337	422	8e-06	52.0
2004112448	2004121539	81.93	83	15	0	193	275	346	428	5e-04	46.1
2004112448	2004092379	81.93	83	15	0	193	275	346	428	5e-04	46.1
2004099281	2004099281	100.00	844	0	0	1	844	1	844	0.0	1661
2004099281	2004142218	90.13	446	43	1	400	844	1	446	1e-149	 529
2004099281	2004092058	81.88	458	82	1	376	832	76	533	1e-63	 244
2004099281	2004147330	83.64	110	18	0	424	533	541	650	6e-13	75.8
2004099281	2004147330	82.86	70	12	0	230	299	347	416	0.002	44.1
2004099281	2004146484	86.05	86	12	0	685	770	577	662	6e-13	75.8
2004099281	2004146484	85.88	85	12	0	424	508	316	400	2e-12	73.8
2004099281	2004146484	83.10	71	12	0	229	299	121	191	5e-04	46.1
2004099281	2004106112	81.68	131	23	1	694	823	613	743	2e-09	63.9
2004099281	2004147824	85.71	70	10	0	439	508	490	559	4e-08	60.0
2004099281	2004153303	88.64	44	5	0	439	482	619	662	1e-04	48.1
2004099281	2004082897	81.52	92	17	0	664	755	10	101	1e-04	48.1
2004099281	2004142389	89.47	38	4	0	795	832	169	206	0.002	44.1
DATA1
2004082897	2004082897	100.00	810	0	0	1	810	1	810	0.0	1582
2004082897	2004156684	87.74	261	32	0	3	263	153	413	1e-69	 264
2004082897	2004149613	80.35	514	99	2	289	801	1	513	2e-53	 210
2004082897	2004146484	87.91	91	11	0	8	98	554	644	2e-18	93.7
2004082897	2004126309	81.10	164	31	0	8	171	80	243	4e-14	79.8
2004082897	2004106112	85.11	94	14	0	8	101	581	674	6e-13	75.8
2004082897	2004127134	95.45	44	2	0	127	170	745	788	9e-12	71.9
2004082897	2004127134	91.18	34	3	0	223	256	844	877	0.002	44.1
2004082897	2004117857	79.46	185	38	0	621	805	45	229	9e-12	71.9
2004082897	2004142219	87.69	65	8	0	25	89	904	968	6e-10	65.9
2004082897	2004142219	90.57	53	5	0	136	188	1015	1067	6e-10	65.9
2004082897	2004142389	100.00	29	0	0	571	599	601	629	1e-07	58.0
2004082897	2004142389	96.43	28	1	0	143	170	170	197	1e-04	48.1
2004082897	2004092058	83.15	89	15	0	13	101	367	455	1e-07	58.0
2004082897	2004142218	87.27	55	7	0	10	64	265	319	2e-06	54.0
2004082897	2004117248	96.67	30	1	0	142	171	667	696	8e-06	52.0
2004082897	2004125016	96.55	29	1	0	571	599	571	599	3e-05	50.1
2004082897	2004125016	96.15	26	1	0	145	170	142	167	0.002	44.1
2004082897	2004099281	81.52	92	17	0	10	101	664	755	1e-04	48.1
2004082897	2004117249	93.10	29	2	0	571	599	244	272	0.008	42.1
2004083856	2004083856	100.00	774	0	0	1	774	1	774	0.0	1534
2004083856	2004128009	87.09	767	84	3	13	764	412	1178	0.0	 735
2004083856	2004100486	89.04	365	40	0	408	772	123	487	1e-112	 406
2004083856	2004112466	91.47	211	18	0	1	211	598	808	3e-73	 276
2004083856	2004147543	84.54	194	30	0	346	539	871	1064	2e-34	 147
2004083856	2004131474	84.74	190	29	0	346	535	886	1075	2e-34	 147
2004083856	2004131474	87.80	41	5	0	61	101	613	653	0.008	42.1
2004083856	2004131474	82.61	69	12	0	138	206	690	758	0.008	42.1
2004083856	2004097313	89.36	94	10	0	679	772	76	169	2e-22	 107
2004083856	2004149567	90.91	44	4	0	73	116	235	278	5e-07	56.0
DATA2

iterblast();

sub iterblast {
    # settings
    my $myblast = "blastall -p blastn -m 8";
    my $blastdb = 'foo';
    my $evalue     = 0.01;
    my $wordsize   = 11;
    my $roundlimit = 4;

    print <<LOGMSG;
Configurations:
Output files     : xxx\-
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;
    my @fastaDbs;

    # Start the iterative blastn rounds
    for my $round (1 .. @roundData) {
        open my $parse, '<', \$roundData[$round - 1];

        push @fastaDbs, '';
        open my $fasta, '>', \$fastaDbs[-1];

        # parse blast output (tab form) and add matched id's in hits hash
        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 fasta file
        my $hitcount;

        for my $hit (keys %hits) {
            next if exists $queryids{$hit};

            # only write uniq ids to file
            print $fasta "fastacmd -d $blastdb -s 'lcl|$hit'\n";
            $hitcount++;
        }

        close $fasta;
        close $parse;

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

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

    print '-' x 20, "\n$_\n" for @fastaDbs;
    print "Total uniq hits found in all rounds: ", scalar keys %hits, "\n";
}