# Creates BioPerl input sequence stream.
my $in_seq = Bio::SeqIO->new(-file   => "<$input_file", -format => $seq_format );

# Extracting sequences from stream.
print("- reading and translating sequences...\n");
my $seq_counter = 0;
my $unique_count = 0;
my @translated_seqs;

while (my $seq = $in_seq->next_seq()) 
{
    
    $seq_counter++;
    print("-\tsequences read: $seq_counter\r");
    
    my $temp_seq;
    
    # Translates sequence and stores the translated sequences if they do not
    # contain any stop codons.
    
    # Reading frames 1, 2 and 3.
    $temp_seq = $seq->translate();
    $temp_seq->display_id("test_id-$unique_count");
    $unique_count++;
    push(@translated_seqs, $temp_seq) unless ($temp_seq->seq() =~ /\*+/);
    $temp_seq = $seq->translate(-frame => 1);
    $temp_seq->display_id("test_id-$unique_count");
    $unique_count++;
    push(@translated_seqs, $temp_seq) unless ($temp_seq->seq() =~ /\*+/);
    $temp_seq = $seq->translate(-frame => 2);
    $temp_seq->display_id("test_id-$unique_count");
    $unique_count++;
    push(@translated_seqs, $temp_seq) unless ($temp_seq->seq() =~ /\*+/);

    # Creates the reverse complement sequence.
    my $rc_seq = $seq->revcom();
    
    # Reading frames -1, -2, and -3
    $temp_seq = $rc_seq->translate();
    $temp_seq->display_id("test_id-$unique_count");
    $unique_count++;
    push(@translated_seqs, $temp_seq) unless ($temp_seq->seq() =~ /\*+/);
    $temp_seq = $rc_seq->translate(-frame => 1);
    $temp_seq->display_id("test_id-$unique_count");
    $unique_count++;
    push(@translated_seqs, $temp_seq) unless ($temp_seq->seq() =~ /\*+/);
    $temp_seq = $rc_seq->translate(-frame => 2);
    $temp_seq->display_id("test_id-$unique_count");
    $unique_count++;
    push(@translated_seqs, $temp_seq) unless ($temp_seq->seq() =~ /\*+/);
    
}

# Blasting...
my @params = (-program => 'blastp', -database => '/share/raid1/database/ftp.ncbi.nih.gov/blast/db/20090602/nr', -expectation => '200000', -Word => '2', -Matrix => 'PAM30', -Gapcost => '9.1', -FilterString => 'F', _READMETHOD => 'blasttable' , -m => '8', -outfile => 'blast.out');
my $blaster = Bio::Tools::Run::StandAloneBlast->new(@params);
my $blast_report = $blaster->blastall(@translated_seqs);

# Parsing results
my $result = $blast_report->next_result();
my $hit = $result->next_hit();