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
|
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
# $Id: BPbl2seq.t,v 1.22 2003/02/03 01:42:35 lapp Exp $
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 108;
}
use Bio::Tools::BPbl2seq;
#use Bio::Tools::BPlite;
use Bio::Root::IO;
ok(1);
my $report = new Bio::Tools::BPbl2seq(-file => Bio::Root::IO->catfile("t","data","bl2seq.out"),
-report_type => 'blastp');
$report->verbose(2);
ok $report->isa('Bio::Tools::BPbl2seq');# " no report";
ok defined($report->sbjctName),1, " no hit";
my $hsp = $report->next_feature;
ok $hsp->score, 481, "wrong score";
ok $hsp->bits, 191, "wrong score in bits ";
ok int $hsp->percent, 34, "wrong match percent";
ok $hsp->P == 2e-53;# "wrong expectation value ";
ok $hsp->match, 111, "wrong number of matches ";
ok $hsp->positive, 167, "wrong number of positives";
ok $hsp->start, 28, 'wrong starting position';
ok $hsp->end, 343, 'wrong ending position';
ok $hsp->length, 316, "wrong length";
ok $hsp->querySeq =~ /QFL/; #"bad query sequence";
ok $hsp->sbjctSeq =~ /RFAR/;#"bad hit sequence";
ok $hsp->homologySeq =~ /PVKN/;# , "bad homology sequence";
ok $hsp->query->start, 28, "wrong query start";
ok $hsp->query->end, 343, "wrong query end";
ok $hsp->hit->start, 60, "wrong hit start ";
ok $hsp->hit->end, 360, "wrong hit end";
ok $report->sbjctName =~ /ALEU_HORVU/;# "wrong hit name";
$report = new Bio::Tools::BPbl2seq(-file => Bio::Root::IO->catfile("t","data","bl2seq.bug940.out"),
-report_type => 'blastp');
$report->verbose(2);
ok $report->isa('Bio::Tools::BPbl2seq');# " no report";
ok defined($report->sbjctName),1, " no query";
$hsp = $report->next_feature;
ok $hsp->score, 1626, "wrong score";
ok $hsp->bits, 637, "wrong score in bits ";
ok int $hsp->percent, 66, "wrong match percent";
ok $hsp->P == 0.0;# "wrong expectation value ";
ok $hsp->match, 311, "wrong number of matches ";
ok $hsp->positive, 330, "wrong number of positives";
ok $hsp->start, 121, 'wrong starting position';
ok $hsp->end, 469, 'wrong ending position';
ok $hsp->length, 349, "wrong length";
ok $hsp->querySeq =~ /^MGN/; #"bad query sequence";
ok $hsp->sbjctSeq =~ /^MGN/;#"bad hit sequence";
ok $hsp->homologySeq =~ /^MGN/;# , "bad homology sequence";
ok $hsp->query->start, 121, "wrong query start";
ok $hsp->query->end, 469, "wrong query end";
ok $hsp->hit->start, 1, "wrong hit start ";
ok $hsp->hit->end, 469, "wrong hit end";
ok $hsp->hit->seq_id =~ /gi|4507985/;# "wrong hit name";
ok $hsp->gaps, 120;
$hsp = $report->next_feature;
ok($hsp);
ok $hsp->score, 1524, "wrong score";
ok $hsp->bits, 598, "wrong score in bits ";
ok int $hsp->percent, 61, "wrong match percent";
ok $hsp->P == 1e-175, 1,"wrong expectation value ";
ok $hsp->match, 275, "wrong number of matches ";
ok $hsp->positive, 324, "wrong number of positives";
ok $hsp->start, 6, 'wrong starting position';
ok $hsp->end, 420, 'wrong ending position';
ok $hsp->length, 415, "wrong length";
ok $hsp->querySeq =~ /^EKPY/; #"bad query sequence";
ok $hsp->sbjctSeq =~ /^EKPY/;#"bad hit sequence";
ok $hsp->homologySeq =~ /^EKPY/;# , "bad homology sequence";
ok $hsp->query->start, 6, "wrong query start";
ok $hsp->query->end, 420, "wrong query end";
ok $hsp->hit->start, 22, "wrong hit start ";
ok $hsp->hit->end, 464, "wrong hit end";
ok $hsp->hit->seq_id =~ /gi|4507985/;# "wrong hit name";
ok $hsp->gaps, 30;
$report = new Bio::Tools::BPbl2seq(-file => Bio::Root::IO->catfile("t","data","empty.bl2seq"),
-report_type => 'blastp');
$report->verbose(2);
ok( $report->isa('Bio::Tools::BPbl2seq'),1, " no report found");
ok $report->sbjctName, '',"subject found where none expected";
# test for strandedness on dna alignment reports
$report = new Bio::Tools::BPbl2seq(-file => Bio::Root::IO->catfile(qw(t data bl2seq.blastn)),
-report_type => 'blastn');
ok $report->isa('Bio::Tools::BPbl2seq');# " no report";
ok $report->sbjctName,'human', " no subject";
$hsp = $report->next_feature;
ok $hsp->score, 27, "wrong score";
ok $hsp->bits, '54.0', "wrong score in bits ";
ok int $hsp->percent, 88, "wrong match percent";
ok $hsp->P, '2e-12';# "wrong expectation value ";
ok $hsp->match, 83, "wrong number of matches ";
ok $hsp->positive, 83, "wrong number of positives";
ok $hsp->start, 94, 'wrong starting position';
ok $hsp->end, 180, 'wrong ending position';
ok $hsp->strand, 1, "wrong query strand";
ok $hsp->length, 87, "wrong length";
ok $hsp->querySeq =~ /^gtggc/; #"bad query sequence";
ok $hsp->sbjctSeq =~ /^gtggc/;#"bad hit sequence";
ok $hsp->homologySeq =~ /^\|\|\|\|/;# , "bad homology sequence";
ok $hsp->query->start, 94, "wrong query start";
ok $hsp->query->end, 180, "wrong query end";
ok $hsp->query->strand, 1, "wrong query strand";
ok $hsp->hit->start, 86, "wrong hit start ";
ok $hsp->hit->end, 179, "wrong hit end";
ok $hsp->hit->strand,1, "wrong hit strand";
ok $hsp->hit->seq_id =~ /human/;# "wrong hit name";
ok $hsp->gaps, 7;
$report = new Bio::Tools::BPbl2seq(-file => Bio::Root::IO->catfile(qw(t data bl2seq.blastn.rev)),
-report_type => 'blastn');
ok $report->isa('Bio::Tools::BPbl2seq');# " no report";
ok $report->sbjctName,'human', " no subject";
$hsp = $report->next_feature;
ok($hsp);
ok $hsp->score, 27, "wrong score";
ok $hsp->bits, '54.0', "wrong score in bits ";
ok int $hsp->percent, 88, "wrong match percent";
ok $hsp->P, '2e-12';# "wrong expectation value ";
ok $hsp->match, 83, "wrong number of matches ";
ok $hsp->positive, 83, "wrong number of positives";
ok $hsp->start, 94, 'wrong starting position';
ok $hsp->end, 180, 'wrong ending position';
ok $hsp->strand, 1, "wrong query strand";
ok $hsp->length, 87, "wrong length";
ok $hsp->querySeq =~ /^gtggc/; #"bad query sequence";
ok $hsp->sbjctSeq =~ /^gtggc/;#"bad hit sequence";
ok $hsp->homologySeq =~ /^\|\|\|\|/;# , "bad homology sequence";
ok $hsp->query->start,94, "wrong query start";
ok $hsp->query->end, 180, "wrong query end";
ok $hsp->query->strand, 1, "wrong query strand";
ok $hsp->hit->start, 1, "wrong hit start ";
ok $hsp->hit->end, 94, "wrong hit end";
ok $hsp->hit->strand,-1, "wrong hit strand";
ok $hsp->hit->seq_id =~ /human/;# "wrong hit name";
ok $hsp->gaps, 7;
|
