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# -*-Perl-*- Test Harness script for Bioperl
# $Id: RemoteBlast_rpsblast.t 16090 2009-09-15 21:57:56Z cjfields $
# malcolm_cook@stowers.org: this test is in a separate file from
# RemoteBlast.t (on which it is modelled) since there is some sort of
# side-effecting between the multiple remote blasts that is causing
# this test to fail, if it comes last, or the other test to fail, if
# this one comes first. THIS IS A BUG EITHER IN REMOTE BLAST OR MY
# UNDERSTANDING, i.e. of how to initialize it.
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 3,
-requires_modules => [qw(IO::String LWP LWP::UserAgent)],
-requires_networking => 1);
use_ok('Bio::Tools::Run::RemoteBlast');
}
my $v = test_debug();
my $inputfilename = test_input_file('ecolitst.fa');
ok( -e $inputfilename);
my $remote_rpsblast = Bio::Tools::Run::RemoteBlast->new
('-verbose' => test_debug(),
'-prog' => 'blastp',
'-data' => 'cdsearch/cdd',
'-readmethod' => 'blasttable',
'-expect' => '1e-10',
);
$remote_rpsblast->retrieve_parameter('ALIGNMENT_VIEW', 'Tabular');
# This is the key to getting job run using rpsblast:
$Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast';
ok($remote_rpsblast->submit_blast($inputfilename),'rpsblast blasttable submitted');
print STDERR "waiting..." if( $v > 0 );
while ( my @rids = $remote_rpsblast->each_rid ) {
foreach my $rid ( @rids ) {
my $rc = $remote_rpsblast->retrieve_blast($rid);
if ( !ref($rc) ) {
if ( $rc < 0 ) {
die "need a better solution for when 'Server failed to return any data'";
}
$remote_rpsblast->remove_rid($rid);
print STDERR "." if ( $v > 0 );
sleep 5;
} else {
ok(1,'retrieve_blast succeeded');
$remote_rpsblast->remove_rid($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 ", $hsp->bits, "\n";
}
}
}
is($count, 44, 'correct result count'); # of course, this could change whenever CDD changes
}
}
}
# To be a good citizen, we should restore the default NCBI service
# ('plain') for future tests
$Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'plain';
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