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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: StandAloneBlast.t,v 1.16.2.5 2002/03/15 18:41:25 jason Exp $
#
use strict;
use constant NUMTESTS => 10;
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => NUMTESTS;
}
END {
foreach( $Test::ntest..NUMTESTS) {
skip('Blast or env variables not installed correctly',1);
}
unlink('blastreport.out');
}
use Bio::Tools::BPlite;
use Bio::Tools::Run::StandAloneBlast;
use Bio::SeqIO;
use Bio::AlignIO;
use Bio::Seq;
use Bio::Root::IO;
use Bio::SearchIO;
ok(1);
my $verbose = -1;
my ($blast_report, $hsp, @testresults);
my $nt_database = 'ecoli.nt';
my $amino_database = 'swissprot';
my @params = ('program' => 'blastn', 'database' => $nt_database ,
'_READMETHOD' => 'SearchIO',
'output' => 'blastreport.out');
my $factory = Bio::Tools::Run::StandAloneBlast->new('-verbose' => $verbose,
@params);
ok $factory;
my $inputfilename = Bio::Root::IO->catfile("t","data","test.txt");
my $program = 'blastn';
my $blast_present = Bio::Tools::Run::StandAloneBlast->exists_blast();
if( ! $blast_present ) {
skip('Blast not installed',1);
exit;
} else {
ok($blast_present);
}
if( ! defined $Bio::Tools::Run::StandAloneBlast::DATADIR ) {
print STDERR "must have BLASTDIR and BLASTDB or BLASTDATADIR env variable set\n";
exit();
}
my $nt_database_file = Bio::Root::IO->catfile($Bio::Tools::Run::StandAloneBlast::DATADIR, $nt_database);
ok($nt_database_file, qr/$nt_database/);
my $amino_database_file = Bio::Root::IO->catfile($Bio::Tools::Run::StandAloneBlast::DATADIR, $amino_database);
my $file_present = -e $nt_database_file;
my $file_present2 = -e $amino_database_file;
unless ($blast_present && $file_present && $file_present2) {
warn "blast program or databases [$nt_database,$amino_database] not found. Skipping rest of tests\n";
exit 0;
}
if ($nt_database eq 'ecoli.nt') {
$testresults[3] = '$blast_report->num_hits == 1' ;
$testresults[4] = '$hsp->score == 182';
$testresults[5] = '$hsp->score == 182';
} else {
$testresults[3] = '$blast_report->num_hits';
$testresults[4] = '$hsp->score';
$testresults[5] = '$hsp->score';
}
if ($amino_database eq 'swissprot') {
$testresults[8] = '$blast_report->number_of_iterations == 2';
} else {
$testresults[8] = '$blast_report->number_of_iterations';
}
$blast_report = $factory->blastall($inputfilename);
ok $testresults[3];
$factory->_READMETHOD('BPlite'); # Note required leading underscore in _READMETHOD
my $str = Bio::SeqIO->new(-file=>Bio::Root::IO->catfile("t","data","dna2.fa") , '-format' => 'Fasta', );
my $seq1 = $str->next_seq();
my $seq2 = $str->next_seq();
my $BPlite_report = $factory->blastall($seq1);
my $sbjct = $BPlite_report->nextSbjct;
$hsp = $sbjct->nextHSP;
ok $testresults[4];
my @seq_array =($seq1,$seq2);
my $seq_array_ref = \@seq_array;
my $BPlite_report2 = $factory->blastall(\@seq_array);
$sbjct = $BPlite_report2->nextSbjct;
$hsp = $sbjct->nextHSP;
ok $testresults[5];
@params = ('-verbose' => $verbose,
'program' => 'blastp'); # This used to be blastp but atleast on my implementation it should be T
$factory = Bio::Tools::Run::StandAloneBlast->new(@params);
$str = Bio::SeqIO->new(-file=>Bio::Root::IO->catfile("t","data","amino.fa") , '-format' => 'Fasta', );
my $seq3 = $str->next_seq();
my $seq4 = $str->next_seq();
my $bl2seq_report = $factory->bl2seq($seq3, $seq4);
$hsp = $bl2seq_report->next_feature;
ok $hsp->hit()->start, 167, " failed creating or parsing bl2seq report object";
@params = ('database' => $amino_database);
$factory = Bio::Tools::Run::StandAloneBlast->new(@params);
my $iter = 2;
$factory->j($iter); # 'j' is blast parameter for # of iterations
my $new_iter = $factory->j();
ok $new_iter, 2, " failed setting blast parameter";
$blast_report = $factory->blastpgp($seq3);
ok $testresults[8];
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