use strict;
use Bio::SeqIO;
use Bio::Tools::Run::StandAloneBlast;
my %srna;
my %genome;
my $seqio_srna = Bio::SeqIO->new(- file=>'/home/jayakuma/script/graphics/JH_TCV_lateSL.clones.filtered.23_1_2008.fa',
				 -format=>'fasta') or die "cannot open file\n";
my $seqio_large = Bio::SeqIO->new(-file => '/home/jayakuma/script/graphics/TCV-jagger.fna',
				  -format =>'fasta') or die " cannot opne the file\n";

while (my $large_seq = $seqio_large->next_seq()){
    my $id = $large_seq->display_id;
    my $seq = $large_seq->seq;
    $genome{$id} = $seq;
    
    while (my $seq_srna = $seqio_srna->next_seq()){
	my $display_id = $seq_srna->display_id;
	my $seq = $seq_srna->seq;
	$srna{$display_id} = $seq;
	#rint "seq: $seq\n";
    }
    
    foreach my $seq_id (keys %srna){
    my $srnas = $srna{$seq_id};
    print "srnas: $srnas\n";
    
    foreach($srnas){
	my $blast = Bio::Tools::Run::StandAloneBlast->new(program=>'blastn',database=>'/home/jayakuma/script/graphics/TCV-jagger.fna');
	my $input = Bio::Seq->new(-seq=> $srnas);
	print $input->seq, "\n";
	my $blast_report = $blast->blastall($input);
	while (my $result = $blast_report->next_result()){
	    my $query_length = $result->query_length();
	    while (my $hit = $result->next_hit()){
		my $id = $hit->accession();
		while (my $hsp = $hit->next_hsp()){
		    if($hsp->frac_identical ==1 && $hsp ->length ==$query_length){
			    print "$srnas\t$id\n";
			}
		}
	    }
	}
    }
}

}



##</code><code>##

srnas: TTTGCAGTATTGGACAAGCC
TTTGCAGTATTGGACAAGCC
Use of uninitialized value in pattern match (m//) at /usr/share/perl5/Bio/SeqIO/fasta.pm line 193, <GEN0> line 81643.
Use of uninitialized value in print at /usr/share/perl5/Bio/Root/IO.pm line 407, <GEN0> line 81643.

-------------------- WARNING ---------------------
MSG: cannot find path to blastall
---------------------------------------------------
Can't call method "next_result" on an undefined value at aligning.pl line 34, <GEN0> line 81643.