#!/usr/bin/perl -w

use strict;
use warnings;
use Bio::SeqIO;
use Bio::Tools::Run::RemoteBlast;
use Bio::Seq;
use IO::String;
use Bio::SearchIO;


use lib qw(/usr/local/bioperl/bioperl-1.5.1);


my $prog   = 'blastp';
my $db     = 'swissprot';              &n
bsp;              &n
bsp;  
my $e_val  = '20000';
my $matrix =  'pam30';              &n
bsp;              &n
bsp;          my $wordSize = '2';


my @data;
my $line_dataArray;
my $rid;
my $count = 1;              &nbs
p;              &nbs
p;                   
my @params = (
  '-prog'   => $prog,
  '-data'   => $db,
  '-expect' => $e_val,
  '-MATRIX_NAME' => $matrix,
  '-readmethod' => 'xml',
  '-WORD_SIZE' => $wordSize,
);

my $seqio_obj = Bio::SeqIO->new(
  -file   => "aloneblosum80.txt",
  -format => "raw",
);

print "entering blast....";

my $xmlFactory = Bio::Tools::Run::RemoteBlast->new(@params);

$Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '9 1';              &n
bsp;              &n
bsp;       $Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = '1000';
   $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'ALIGNMENTS'} = '1000';
    $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'FORMAT_TYPE'} = 'XML';
   

print "Blast entered successfully \n";

while ( my $query = $seqio_obj->next_seq ) {
  print "submit Sequence...just do it....\n";
 
  my $r = $xmlFactory->submit_blast($query);
  print $query->seq;
  print "\n";
 
 
#    sleep 30;

  # Wait for the reply and save the output file
  print "entering while loop for saving Output.... \n";
 
  while ( my @rids = $xmlFactory->each_rid ) {
      foreach my $rid (@rids) {
           
          my $rc = $xmlFactory->retrieve_blast($rid);
          if ( !ref($rc) ) {
              print '$rc is not a ref!', "\n";
              if ( $rc < 0 ) {
                  print "Remove rid ...\n";
                  $xmlFactory->remove_rid($rid);
              }
              # sleep 5;
          }
          else {

              print "retrieved Results successfully \n";
              print $rid;
              print "\n";
              my $filename = "$count.xml";
              $xmlFactory->save_output($filename);
              print "File saved successfully \n";
              my $checkinput = $xmlFactory->file;
              open(my $fh,"<$checkinput") or die $!;
              while(<$fh>){
                print;
              }
              close $fh;
              $count++;
              $xmlFactory->remove_rid($rid);
          }
      }
      print "\n";
      print "\n";

  }
}

[Hubert@ppc9 ~]$ perl -V
Summary of my perl5 (revision 5 version 8 subversion 8) configuration:
  Platform:
    osname=linux, osvers=2.6.16-1.2122_fc5smp, archname=i686-linux
    uname='linux ppc9.bio.ucalgary.ca 2.6.16-1.2122_fc5smp #1 smp sun may 21 15:18:32 edt 2006 i686 i686 i386 gnulinux '
    config_args='-de'
    hint=recommended, useposix=true, d_sigaction=define
    usethreads=undef use5005threads=undef useithreads=undef usemultiplicity=undef
    useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
    use64bitint=undef use64bitall=undef uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='cc', ccflags ='-fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
    optimize='-O2',
    cppflags='-fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include'
    ccversion='', gccversion='4.1.1 20060525 (Red Hat 4.1.1-1)', gccosandvers=''    intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
    ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
    alignbytes=4, prototype=define
  Linker and Libraries:
    ld='cc', ldflags =' -L/usr/local/lib'
    libpth=/usr/local/lib /lib /usr/lib
    libs=-lnsl -ldb -ldl -lm -lcrypt -lutil -lc
    perllibs=-lnsl -ldl -lm -lcrypt -lutil -lc
    libc=/lib/libc-2.4.so, so=so, useshrplib=false, libperl=libperl.a
    gnulibc_version='2.4'
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
    cccdlflags='-fpic', lddlflags='-shared -L/usr/local/lib'


Characteristics of this binary (from libperl):
  Compile-time options: PERL_MALLOC_WRAP USE_LARGE_FILES USE_PERLIO
  Built under linux
  Compiled at Jun  7 2006 18:56:48
  @INC:
    /usr/local/lib/perl5/5.8.8/i686-linux
    /usr/local/lib/perl5/5.8.8
    /usr/local/lib/perl5/site_perl/5.8.8/i686-linux
    /usr/local/lib/perl5/site_perl/5.8.8
    /usr/local/lib/perl5/site_perl
    .
[Hubert@ppc9 ~]$

[Hubert@ppc9 ~]$ which perl
/usr/local/bin/perl
[Hubert@ppc9 ~]$

use lib qw(/home/Hubert/Software/bioperl/bioperl-live/);

Bio::SearchIO: blastxml cannot be found
Exception
------------- EXCEPTION  -------------
MSG: Failed to load module Bio::SearchIO::blastxml. Can't locate XML/SAX.pm in @INC (@INC contains: /usr/local/lib/perl5/5.8.8/i686-linux /usr/local/lib/perl5/5.8.8 /usr/local/lib/perl5/site_perl/5.8.8/i686-linux /usr/local/lib/perl5/site_perl/5.8.8 /usr/local/lib/perl5/site_perl .) at /usr/local/lib/perl5/site_perl/5.8.8/Bio/SearchIO/blastxml.pm line 93.
BEGIN failed--compilation aborted at /usr/local/lib/perl5/site_perl/5.8.8/Bio/SearchIO/blastxml.pm line 93.