1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
|
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: StandAloneBlast.t,v 1.22 2003/11/07 10:12:24 allenday Exp $
#
use strict;
use constant NUMTESTS => 16;
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;
my $verbose = -1;
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 = $factory->executable('blastall');
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(0);
}
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 $exit;
unless ($file_present) {
skip("Blast Database $nt_database not found",1);
# warn "Blast Database $nt_database not found";
$exit = 1;
}
my $file_present2 = -e $amino_database_file;
unless ($file_present2) {
skip("Blast Database $amino_database not found",1);
# warn "Blast Database $amino_database not found";
$exit=1;
}
if ($exit) {
skip("Blast databases(s) not found, skipping remaining tests",1);
# warn "Blast databases(s) not found, skipping remaining tests";
exit(0);
}
my @testresults = qw(37 182 182 253 167 2);
my $testcount = 0;
my $parser = $factory->blastall($inputfilename);
my $blast_report = $parser->next_result;
ok($blast_report->num_hits,$testresults[$testcount++]);
$factory->_READMETHOD('BPlite'); # Note required leading underscore in _READMETHOD
my $str = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile(qw(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;
my $hsp = $sbjct->nextHSP;
ok($hsp->score, $testresults[$testcount]);
$factory->_READMETHOD('Blast');
my $searchio_report = $factory->blastall($seq1);
$sbjct = $searchio_report->next_result->next_hit;
$hsp = $sbjct->next_hsp;
ok($hsp->score, $testresults[$testcount++]);
my @seq_array =($seq1,$seq2);
my $seq_array_ref = \@seq_array;
$factory->_READMETHOD('BPlite');
my $BPlite_report2 = $factory->blastall($seq_array_ref);
$sbjct = $BPlite_report2->nextSbjct;
$hsp = $sbjct->nextHSP;
ok($hsp->score, $testresults[$testcount]);
$factory->_READMETHOD('Blast');
$searchio_report = $factory->blastall($seq_array_ref);
$sbjct = $searchio_report->next_result->next_hit;
$hsp = $sbjct->next_hsp;
ok($hsp->score, $testresults[$testcount++]);
$sbjct = $searchio_report->next_result->next_hit;
ok($sbjct);
$hsp = $sbjct->next_hsp;
ok($hsp->score, $testresults[$testcount++]);
@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(qw(t data amino.fa)),
'-format' => 'Fasta' );
my $seq3 = $str->next_seq();
my $seq4 = $str->next_seq();
$factory->_READMETHOD('BPlite');
my $bl2seq_report = $factory->bl2seq($seq3, $seq4);
$hsp = $bl2seq_report->next_feature;
ok ($hsp->hit->start, $testresults[$testcount],
" failed creating or parsing BPlite bl2seq report object");
$factory->_READMETHOD('Blast');
$bl2seq_report = $factory->bl2seq($seq3, $seq4);
$hsp = $bl2seq_report->next_result->next_hit->next_hsp;
ok( $hsp->hit->start, $testresults[$testcount++],
" failed creating or parsing SearchIO bl2seq report object");
@params = ('database' => $amino_database,
'-verbose' => $verbose);
$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)->next_result;
ok($blast_report->number_of_iterations, $testresults[$testcount]);
$factory->_READMETHOD('BPlite');
$iter = 2;
$factory->j($iter); # 'j' is blast parameter for # of iterations
$new_iter = $factory->j();
ok($new_iter, $iter, " failed setting blast parameter");
$blast_report = $factory->blastpgp($seq3);
ok($blast_report->number_of_iterations, $testresults[$testcount]);
|
