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
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: bl2seq.t 14971 2008-10-28 16:08:52Z cjfields $
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 7);
use_ok('Bio::AlignIO::bl2seq');
}
my $DEBUG = test_debug();
my ($str,$aln,$strout,$status);
# BL2SEQ
$str = Bio::AlignIO->new(-file => test_input_file("bl2seq.out"),
-format => 'bl2seq',
-report_type => 'blastp');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(2)->get_nse, 'ALEU_HORVU/60-360', "BLAST bl2seq format test";
# Bug 2978, test report_type guessing for TBLASTN and correct Frame assignment to HitFrame
$str = Bio::AlignIO->new(-file => test_input_file("bl2seq.tblastn.out"),
-format => 'bl2seq');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
foreach my $seq ( $aln->each_seq_with_id('WAN03UHTX_1') ) {
is $seq->start(), 946;
is $seq->end(), 990;
is $seq->strand(), -1;
}
|
