t/StandAloneBlast.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5 use File::Spec;
   6
   7 BEGIN {
   8         use lib 't/lib';
   9     use BioperlTest;
  10
  11     test_begin(-tests => 45);
  12
  13         use_ok('Bio::Tools::Run::StandAloneBlast');
  14         use_ok('Bio::SeqIO');
  15 }
  16
  17 # Note: the swissprot and ecoli.nt data sets may be downloaded from
  18 # ftp://ftp.ncbi.nih.gov/blast/db/FASTA
  19 my $verbose = test_debug() || -1;
  20 my $nt_database = 'ecoli.nt';
  21 my $amino_database = 'swissprot';
  22 my $evalue = 0.001;
  23 my ($seq1,$seq2,$seq3,$seq4);
  24
  25 # Tests to check that "-attr" and "attr" and "a" all do the same thing
  26 # http://bugzilla.open-bio.org/show_bug.cgi?id=1912
  27 for my $p (qw(database db -d -database d)) {
  28   my $f = Bio::Tools::Run::StandAloneBlast->new($p => $nt_database);
  29   is $f->d(), $nt_database;
  30 }
  31 for my $p (qw(expect evalue -e -expect e)) {
  32   my $f = Bio::Tools::Run::StandAloneBlast->new($p => $evalue);
  33   is $f->e(), $evalue;
  34 }
  35
  36 # NCBI blast params are case-sensitive, wublast aren't
  37 my $ncbi_factory = Bio::Tools::Run::StandAloneBlast->new(-program => 'blastn');
  38 isa_ok $ncbi_factory, 'Bio::Tools::Run::StandAloneBlast';
  39 isa_ok $ncbi_factory, 'Bio::Tools::Run::StandAloneNCBIBlast';
  40 my $wu_factory = Bio::Tools::Run::StandAloneBlast->new(-program => 'wublastn');
  41 isa_ok $wu_factory, 'Bio::Tools::Run::StandAloneBlast';
  42 isa_ok $wu_factory, 'Bio::Tools::Run::StandAloneWUBlast';
  43 for my $p (qw(e E)) {
  44   $ncbi_factory->$p($p);
  45   $wu_factory->$p($p);
  46 }
  47 is $ncbi_factory->e, 'e';
  48 is $ncbi_factory->E, 'E';
  49 is $wu_factory->e, 'E';
  50 is $wu_factory->E, 'E';
  51
  52 # blastall switches like -I should take boolean but return 'T' or 'F' once set
  53 is $ncbi_factory->I, undef;
  54 is $ncbi_factory->I(1), 'T';
  55 is $ncbi_factory->I(0), 'F';
  56 is $ncbi_factory->I('T'), 'T';
  57 is $ncbi_factory->I('F'), 'F';
  58
  59 # We should be able to set -F "m D" in an intuitive way, and also by manually
  60 # quoting the value ourselves
  61 $ncbi_factory->F('m D');
  62 my $param_string = $ncbi_factory->_setparams('blastall');
  63 like $param_string, qr/-F "m D"/;
  64 $ncbi_factory->F('"m S"');
  65 $param_string = $ncbi_factory->_setparams('blastall');
  66 like $param_string, qr/-F "m S"/;
  67 $ncbi_factory->F("'m D'");
  68 $param_string = $ncbi_factory->_setparams('blastall');
  69 like $param_string, qr/-F 'm D'/;
  70
  71 # dashed parameters should work
  72 my $outfile = test_output_file();
  73 ok my $factory = Bio::Tools::Run::StandAloneBlast->new(-verbose     => $verbose,
  74                                                                                                            -program     => 'blastn',
  75                                                                                                            -database    => $nt_database ,
  76                                                                                                            -_READMETHOD => 'SearchIO',
  77                                                                                                            -output      => $outfile,
  78                                                                                                            -verbose     => 0);
  79 is $factory->database, $nt_database;
  80
  81 # Setup and then do tests that actually run blast
  82
  83 my @params = ('program'     => 'blastn',
  84                           'database'    => $nt_database ,
  85                           '_READMETHOD' => 'SearchIO',
  86                           'output'      => $outfile,
  87                           'verbose'     => 0 );
  88 ok $factory = Bio::Tools::Run::StandAloneBlast->new('-verbose' => $verbose, @params);
  89
  90 my $inputfilename = test_input_file('test.txt');
  91
  92 is $factory->quiet(0), 0;
  93 is $factory->q(-3), -3;
  94
  95 SKIP: {
  96         skip 'blastall not installed, skipping tests', 12 unless $factory->executable('blastall');
  97         skip 'must have BLASTDIR, BLASTDB or BLASTDATADIR env variable set, skipping tests', 12 unless defined $Bio::Tools::Run::StandAloneBlast::DATADIR;
  98
  99         my @testresults = qw(37 182 182  253 167 2);
 100         my $testcount = 0;
 101
 102         # use ecoli.nt
 103         my $nt_database_file = File::Spec->catfile($Bio::Tools::Run::StandAloneBlast::DATADIR, $nt_database);
 104         like $nt_database_file, qr/$nt_database/;
 105         SKIP: {
 106                 skip "Database $nt_database not found, skipping tests on it", 8 unless -e $nt_database_file;
 107
 108                 my $parser = $factory->blastall($inputfilename);
 109                 my $blast_report = $parser->next_result;
 110                 is $blast_report->num_hits, $testresults[$testcount++];
 111
 112                 $factory->_READMETHOD('blast_pull');  # Note required leading underscore in _READMETHOD
 113                 my $str = Bio::SeqIO->new('-file' => test_input_file('dna2.fa'),
 114                                                                   '-format' => 'fasta');
 115                 $seq1 = $str->next_seq();
 116                 $seq2 = $str->next_seq();
 117
 118                 my $pull_report = $factory->blastall($seq1);
 119                 my $sbjct = $pull_report->next_result->next_hit;
 120                 my $hsp = $sbjct->next_hsp;
 121                 is $hsp->score, $testresults[$testcount];
 122
 123                 $factory->_READMETHOD('Blast');
 124                 my $searchio_report = $factory->blastall($seq1);
 125                 $sbjct = $searchio_report->next_result->next_hit;
 126                 $hsp = $sbjct->next_hsp;
 127                 is $hsp->score, $testresults[$testcount++];
 128
 129                 my @seq_array =($seq1,$seq2);
 130                 my $seq_array_ref = \@seq_array;
 131                 $factory->_READMETHOD('blast_pull');
 132                 $pull_report = $factory->blastall($seq_array_ref);
 133                 $sbjct = $pull_report->next_result->next_hit;
 134                 $hsp = $sbjct->next_hsp;
 135                 is $hsp->score, $testresults[$testcount];
 136
 137                 $factory->_READMETHOD('Blast');
 138                 $searchio_report = $factory->blastall($seq_array_ref);
 139                 $sbjct = $searchio_report->next_result->next_hit;
 140                 $hsp = $sbjct->next_hsp;
 141                 is $hsp->score, $testresults[$testcount++];
 142
 143                 ok $sbjct = $searchio_report->next_result->next_hit;
 144                 $hsp = $sbjct->next_hsp;
 145                 is $hsp->score, $testresults[$testcount++];
 146
 147                 @params = ('-verbose' => $verbose, 'program'  => 'blastp');
 148                 $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
 149
 150                 $str = Bio::SeqIO->new(-file => test_input_file('amino.fa'),
 151                                                            -format => 'Fasta' );
 152                 $seq3 = $str->next_seq();
 153                 $seq4 = $str->next_seq();
 154
 155                 #*** no longer testing BPlite since deprecated, blast_pull doesn't support bl2seq yet
 156                 #$factory->_READMETHOD('BPlite');
 157                 #my $bl2seq_report = $factory->bl2seq($seq3, $seq4);
 158                 #$hsp = $bl2seq_report->next_feature;
 159                 #is $hsp->hit->start, $testresults[$testcount], "creating/parsing BPlite bl2seq report object";
 160
 161                 $factory->_READMETHOD('Blast');
 162                 my $bl2seq_report = $factory->bl2seq($seq3, $seq4);
 163                 $hsp = $bl2seq_report->next_result->next_hit->next_hsp;
 164                 is $hsp->hit->start, $testresults[$testcount++], "creating/parsing SearchIO bl2seq report object";
 165         }
 166
 167         # use swissprot
 168         my $amino_database_file = File::Spec->catfile($Bio::Tools::Run::StandAloneBlast::DATADIR, $amino_database);
 169         SKIP: {
 170                 skip "Database $amino_database not found, skipping tests on it", 3 unless -e $amino_database_file;
 171
 172                 @params = ('database' => $amino_database, '-verbose' => $verbose);
 173                 $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
 174
 175                 my $iter = 2;
 176                 $factory->j($iter);    # 'j' is blast parameter for # of iterations
 177                 my $new_iter = $factory->j();
 178                 is $new_iter, 2, "set blast parameter";
 179
 180                 my $blast_report = $factory->blastpgp($seq3)->next_result;
 181                 is $blast_report->number_of_iterations, $testresults[$testcount];
 182
 183                 $factory->_READMETHOD('blast_pull');
 184                 $iter = 2;
 185                 $factory->j($iter);    # 'j' is blast parameter for # of iterations
 186                 $new_iter = $factory->j();
 187                 is $new_iter, $iter, "set blast parameter";
 188
 189                 #*** no longer testing BPlite since deprecated, blast_pull doesn't support iterations yet
 190                 #$blast_report = $factory->blastpgp($seq3);
 191                 #is $blast_report->number_of_iterations, $testresults[$testcount];
 192         }
 193 }