t/RemoteBlast.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use lib 't/lib';
   8     use BioperlTest;
   9
  10     test_begin(-tests => 16,
  11                -requires_modules => [qw(IO::String LWP LWP::UserAgent)],
  12                -requires_networking => 1);
  13
  14     use_ok('Bio::Tools::Run::RemoteBlast');
  15 }
  16
  17 my $prog = 'blastp';
  18 my $db   = 'swissprot';
  19 my $e_val= '1e-10';
  20 my $v = test_debug();
  21 my $remote_blast = Bio::Tools::Run::RemoteBlast->new('-verbose' => $v,
  22                                                                                                         '-prog' => $prog,
  23                                                                                                         '-data' => $db,
  24                                                                                                         '-expect' => $e_val,
  25                                                           );
  26 $remote_blast->submit_parameter('ENTREZ_QUERY',
  27                                                                                   'Escherichia coli[ORGN]');
  28 my $inputfilename = test_input_file('ecolitst.fa');
  29 ok( -e $inputfilename);
  30
  31 ok(1, 'Text BLAST');
  32
  33 my $r = $remote_blast->submit_blast($inputfilename);
  34 ok($r);
  35 print STDERR "waiting..." if( $v > 0 );
  36 while ( my @rids = $remote_blast->each_rid ) {
  37         foreach my $rid ( @rids ) {
  38                 my $rc = $remote_blast->retrieve_blast($rid);
  39                 if( !ref($rc) ) {
  40                         if( $rc < 0 ) {
  41                                 $remote_blast->remove_rid($rid);
  42                                 # need a better solution for when 'Server failed to return any data'
  43                         }
  44                         print STDERR "." if ( $v > 0 );
  45                         sleep 5;
  46                 } else {
  47                         ok(1);
  48                         $remote_blast->remove_rid($rid);
  49                         my $result = $rc->next_result;
  50                         like($result->database_name, qr/swissprot/i);
  51                         my $count = 0;
  52                         while( my $hit = $result->next_hit ) {
  53                                 $count++;
  54                                 next unless ( $v > 0);
  55                                 print "sbjct name is ", $hit->name, "\n";
  56                                 while( my $hsp = $hit->next_hsp ) {
  57                                         print "score is ", $hsp->score, "\n";
  58                                 }
  59                         }
  60                         is($count, 3);
  61                 }
  62         }
  63 }
  64
  65 # test blasttable
  66
  67 ok(1, 'Tabular BLAST');
  68
  69 my $remote_blast2 = Bio::Tools::Run::RemoteBlast->new
  70   ('-verbose'    => $v,
  71         '-prog'       => $prog,
  72         '-data'       => $db,
  73         '-readmethod' => 'blasttable',
  74         '-expect'     => $e_val,
  75   );
  76 $remote_blast2->submit_parameter('ENTREZ_QUERY', 'Escherichia coli[ORGN]');
  77
  78 $remote_blast2->retrieve_parameter('ALIGNMENT_VIEW', 'Tabular');
  79
  80 $inputfilename = test_input_file('ecolitst.fa');
  81
  82 $r = $remote_blast2->submit_blast($inputfilename);
  83 ok($r);
  84 print STDERR "waiting..." if( $v > 0 );
  85 while ( my @rids = $remote_blast2->each_rid ) {
  86         foreach my $rid ( @rids ) {
  87                 my $rc = $remote_blast2->retrieve_blast($rid);
  88                 if( !ref($rc) ) {
  89                         if( $rc < 0 ) {
  90                                 $remote_blast2->remove_rid($rid);
  91                                 # need a better solution for when 'Server failed to return any data'
  92                         }
  93                         print STDERR "." if ( $v > 0 );
  94                         sleep 5;
  95                 } else {
  96                         ok(1);
  97                         $remote_blast2->remove_rid($rid);
  98                         my $result = $rc->next_result;
  99                         my $count = 0;
 100                         while( my $hit = $result->next_hit ) {
 101                                 $count++;
 102                                 next unless ( $v > 0);
 103                                 print "sbjct name is ", $hit->name, "\n";
 104                                 while( my $hsp = $hit->next_hsp ) {
 105                                         print "score is ", $hsp->score, "\n";
 106                                 }
 107                         }
 108                         is($count, 3);
 109                 }
 110         }
 111 }
 112
 113 SKIP: {
 114     test_skip(-tests => 5, -requires_module => 'Bio::SearchIO::blastxml');
 115
 116         my $remote_blastxml = Bio::Tools::Run::RemoteBlast->new('-prog' => $prog,
 117                 '-data'       => $db,
 118                 '-readmethod' => 'xml',
 119                 '-expect'     => $e_val,
 120         );
 121         $remote_blast->submit_parameter('ENTREZ_QUERY',
 122                                                                         'Escherichia coli[ORGN]');
 123
 124         $remote_blastxml->retrieve_parameter('FORMAT_TYPE', 'XML');
 125         $inputfilename = test_input_file('ecolitst.fa');
 126
 127         ok(1, 'XML BLAST');
 128
 129         $r = $remote_blastxml->submit_blast($inputfilename);
 130         ok($r);
 131         print STDERR "waiting..." if( $v > 0 );
 132         while ( my @rids = $remote_blastxml->each_rid ) {
 133                 foreach my $rid ( @rids ) {
 134                         my $rc = $remote_blastxml->retrieve_blast($rid);
 135                         if( !ref($rc) ) {
 136                                 if( $rc < 0 ) {
 137                                         $remote_blastxml->remove_rid($rid);
 138                                         # need a better solution for when 'Server failed to return any data'
 139                                 }
 140                                 print STDERR "." if ( $v > 0 );
 141                                 sleep 5;
 142                         } else {
 143                                 ok(1);
 144                                 $remote_blastxml->remove_rid($rid);
 145                                 my $result = $rc->next_result;
 146                                 like($result->database_name, qr/swissprot/i);
 147                                 my $count = 0;
 148                                 while( my $hit = $result->next_hit ) {
 149                                         $count++;
 150                                         next unless ( $v > 0);
 151                                         print "sbjct name is ", $hit->name, "\n";
 152                                         while( my $hsp = $hit->next_hsp ) {
 153                                                 print "score is ", $hsp->score, "\n";
 154                                         }
 155                                 }
 156                                 is($count, 3);
 157                         }
 158                 }
 159         }
 160 }