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# -*-Perl-*- for my emacs
use strict;
use vars qw($NUMTESTS);
my $error;
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
$error = 0;
$NUMTESTS = 6;
plan tests => 6;
eval { require 'IO/String.pm' };
if( $@ ) {
print STDERR "IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests.\n";
for( 1..$NUMTESTS ) {
skip("IO::String not installed. This means the Bio::DB::* modules are not usable. Skipping tests",1);
}
$error = 1;
}
}
my $actually_submit = 0;
if( $error == 1 ) {
exit(0);
}
require Bio::Tools::Run::RemoteBlast;
require Bio::SeqIO;
require Bio::AlignIO;
require Bio::Seq;
require Bio::Root::IO;
ok(1);
my $prog = 'blastp';
my $db = 'ecoli';
my $e_val= '1e-10';
my $v = 0;
my $remote_blast = Bio::Tools::Run::RemoteBlast->new('-verbose' => $v,
'-prog' => $prog,
'-data' => $db,
'-expect' => $e_val,
);
my $inputfilename = Bio::Root::IO->catfile("t","data","ecolitst.fa");
ok( -e $inputfilename);
if( $actually_submit == 0 ) {
print STDERR "Skipping submitting remote BLAST to avoid Time-out\n";
foreach( $Test::ntest..$NUMTESTS) {
skip('Skip to avoid timeout',1);
}
} else {
my $r = $remote_blast->submit_blast($inputfilename);
ok($r);
print STDERR "waiting..." if( $v > 0 );
while ( my @rids = $remote_blast->each_rid ) {
foreach my $rid ( @rids ) {
my $rc = $remote_blast->retrieve_blast($rid);
if( !ref($rc) ) {
if( $rc < 0 ) {
$remote_blast->remove_rid($rid);
ok(0);
}
print STDERR "." if ( $v > 0 );
sleep 5;
} else {
ok(1);
$remote_blast->remove_rid($rid);
my $result = $rc->next_result;
ok($result->database_name, qr/E. coli/);
my $count = 0;
while( my $hit = $result->next_hit ) {
$count++;
next unless ( $v > 0);
print "sbjct name is ", $hit->name, "\n";
while( my $hsp = $hit->next_hsp ) {
print "score is ", $hsp->score, "\n";
}
}
ok($count, 3);
}
}
}
}
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