#!/usr/bin/perl; 

use strict;

# installed bioperl locally, use local bioperl lib
#use lib="/home/murphyr/lib/";

use Bio::Seq; 
use Bio::SeqIO::fasta; 
use Bio::Tools::Blast; 
use Bio::Tools::Run::StandAloneBlast; 
use Bio::Tools::SeqStats; 
use Data::Dumper; 
print "Program to blast subsequences \n"; 

print "Enter File name of Sequence in FASTA Format \n";
my $inputfile = <STDIN>;
print "$inputfile \n";
my $inseq1 = Bio::SeqIO ->new('-file' => "$inputfile", '-format'=> 'fasta');
my $outseq1 = new Bio::SeqIO (-fh  => \*STDOUT, -format => 'fasta');
my $seq1 = $inseq1 -> next_seq();
my $seq_stats1 = Bio::Tools::SeqStats->new(-seq=>$seq1);
my $monomer_ref = $seq_stats1 -> count_monomers();
my @k = keys %$monomer_ref;
my @v = values %$monomer_ref;
print "@k\n";
print "@v\n";
my $mytotal = 0;
foreach my $value (@v) {
    $mytotal = $mytotal + $value;
}

# print "$seq1 -> seq()\n";
my $did = $seq1 -> display_id();

print "$did\n";

print "Here \n";
# print $outseq1 -> write_seq($seq1);

my $start_pos = 0;
my $end_pos = 24;  

while ($end_pos != $mytotal) { 

$start_pos = $start_pos + 1;
$end_pos = $end_pos + 1; 

my $subseq = $seq1 -> subseq($start_pos, $end_pos);

print "$subseq \n"; 

print "Now doing blast on $subseq \n"; 

my @params = ('program'  => 'blastn',
             'database' => 'virus-db',
             'outfile' => "$subseq.out"); 

my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
my $subinput = Bio::Seq->new('-id'=>"sub test query",
                         '-seq'=>"$subseq");
my $blast_report = $factory->blastall($subinput);

# Get the report
my $searchio = new Bio::SearchIO ('-format' => 'blast',
                                 '-file'   => "$subseq.out");
my $result = $searchio->next_result;
# Get info about the entire report
$result->database_name;
my $algorithm_type =  $result->algorithm;
# get info about the first hit
my $hit = $result->next_hit;
my $hit_name = $hit->name ;
# get info about the first hsp of the first hit
my $hsp = $hit->next_hsp;
my $hsp_start = $hsp->query->start;

print "Now parsing the blast reports using SearchIO \n"; 
#
# Not being selective here ... print the whole she-bang! ...
#
print "Algorithm Type \n";  
print "$algorithm_type \n";

while ( (my $khit, my $vhit) = each %{$hit}) { 
     print "$khit => $vhit \n"; 
      } 

print Dumper(\%$hit); 

print "Hit Name \n"; 
print "$hit_name\n";

while ( (my $khit,my $vhit) = each %{$hsp}) {
      if ($khit eq "_evalue") {   
      print "$khit => $vhit \n";
      }  
      }