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# -*-Perl-*- Test Harness script for Bioperl
# $Id: RemoteBlast.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 16,
-requires_modules => [qw(IO::String LWP LWP::UserAgent)],
-requires_networking => 1);
use_ok('Bio::Tools::Run::RemoteBlast');
}
my $prog = 'blastp';
my $db = 'swissprot';
my $e_val= '1e-10';
my $v = test_debug();
my $remote_blast = Bio::Tools::Run::RemoteBlast->new('-verbose' => $v,
'-prog' => $prog,
'-data' => $db,
'-expect' => $e_val,
);
$remote_blast->submit_parameter('ENTREZ_QUERY',
'Escherichia coli[ORGN]');
my $inputfilename = test_input_file('ecolitst.fa');
ok( -e $inputfilename);
ok(1, 'Text BLAST');
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);
# need a better solution for when 'Server failed to return any data'
}
print STDERR "." if ( $v > 0 );
sleep 5;
} else {
ok(1);
$remote_blast->remove_rid($rid);
my $result = $rc->next_result;
like($result->database_name, qr/swissprot/i);
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 ", $hsp->score, "\n";
}
}
is($count, 3);
}
}
}
# test blasttable
ok(1, 'Tabular BLAST');
my $remote_blast2 = Bio::Tools::Run::RemoteBlast->new
('-verbose' => $v,
'-prog' => $prog,
'-data' => $db,
'-readmethod' => 'blasttable',
'-expect' => $e_val,
);
$remote_blast2->submit_parameter('ENTREZ_QUERY', 'Escherichia coli[ORGN]');
$remote_blast2->retrieve_parameter('ALIGNMENT_VIEW', 'Tabular');
$inputfilename = test_input_file('ecolitst.fa');
$r = $remote_blast2->submit_blast($inputfilename);
ok($r);
print STDERR "waiting..." if( $v > 0 );
while ( my @rids = $remote_blast2->each_rid ) {
foreach my $rid ( @rids ) {
my $rc = $remote_blast2->retrieve_blast($rid);
if( !ref($rc) ) {
if( $rc < 0 ) {
$remote_blast2->remove_rid($rid);
# need a better solution for when 'Server failed to return any data'
}
print STDERR "." if ( $v > 0 );
sleep 5;
} else {
ok(1);
$remote_blast2->remove_rid($rid);
my $count = 0;
while (my $result = $rc->next_result) {
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 ", $hsp->score, "\n";
}
}
}
is($count, 3);
}
}
}
SKIP: {
test_skip(-tests => 5, -requires_module => 'Bio::SearchIO::blastxml');
my $remote_blastxml = Bio::Tools::Run::RemoteBlast->new('-prog' => $prog,
'-data' => $db,
'-readmethod' => 'xml',
'-expect' => $e_val,
);
$remote_blastxml->submit_parameter('ENTREZ_QUERY',
'Escherichia coli[ORGN]');
$remote_blastxml->retrieve_parameter('FORMAT_TYPE', 'XML');
$inputfilename = test_input_file('ecolitst.fa');
ok(1, 'XML BLAST');
$r = $remote_blastxml->submit_blast($inputfilename);
ok($r);
print STDERR "waiting..." if( $v > 0 );
while ( my @rids = $remote_blastxml->each_rid ) {
foreach my $rid ( @rids ) {
my $rc = $remote_blastxml->retrieve_blast($rid);
if( !ref($rc) ) {
if( $rc < 0 ) {
$remote_blastxml->remove_rid($rid);
# need a better solution for when 'Server failed to return any data'
}
print STDERR "." if ( $v > 0 );
sleep 5;
} else {
ok(1);
$remote_blastxml->remove_rid($rid);
my $result = $rc->next_result;
like($result->database_name, qr/swissprot/i);
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 ", $hsp->score, "\n";
}
}
is($count, 3);
}
}
}
}
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