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# -*-Perl-*- Test Harness script for Bioperl
# $Id: SeqPattern.t 16139 2009-09-18 21:11:23Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 28);
use_ok('Bio::Tools::SeqPattern');
}
my ( $pattern,$pattern_obj,$pattern_obj2, $pattern_obj3);
$pattern = '(CCCCT)N{1,200}(agyyg)N{1,80}(ag)';
ok $pattern_obj = Bio::Tools::SeqPattern->new(-SEQ =>$pattern, -TYPE =>'dna');
isa_ok $pattern_obj, 'Bio::Tools::SeqPattern';
$pattern_obj2 = $pattern_obj->revcom();
is $pattern_obj2->str, '(CT)N(CRRCT){1,80}N(AGGGG){1,200}';
$pattern_obj3 = $pattern_obj->revcom(1);
is $pattern_obj3->str, '(CT).{1,80}(C[GA][GA]CT).(AGGGG){1,200}';
$pattern = '(CCCCT)N{1,200}(agyyg)N{1,80}(bb)'; # test protein object expand
ok $pattern_obj = Bio::Tools::SeqPattern->new(-SEQ =>$pattern, -TYPE =>'protein');
isa_ok $pattern_obj, 'Bio::Tools::SeqPattern';
is $pattern_obj2->expand, '(CT).(C[AG][AG]CT){1,80}.(AGGGG){1,200}';
# amino patterns
$pattern = 'ABZH';
$pattern_obj2 = Bio::Tools::SeqPattern->new(-SEQ =>$pattern,
-TYPE =>'amino');
is $pattern_obj2->expand, 'A[EQ][DN]H';
SKIP: {
test_skip(-tests => 19, -requires_module => 'List::MoreUtils');
# Test reverse complement
my $rev_pattern = $pattern_obj2->backtranslate;
isa_ok $rev_pattern, 'Bio::Tools::SeqPattern';
is $rev_pattern->str, 'GCNRAYSARCAY';
# Test exceptions.
throws_ok { $pattern_obj2->revcom } qr/revcom for .+ sequence types/;
throws_ok { $rev_pattern->backtranslate } qr/backtranslate for .+ sequence types/;
# Test reverse translation more thoroughly
my @data;
while (<DATA>) {
chomp;
push @data, [ split ];
}
foreach my $line (@data) {
my $pattern_obj = Bio::Tools::SeqPattern->new(
-SEQ => $line->[0],
-TYPE => 'amino',
);
isa_ok $pattern_obj, 'Bio::Tools::SeqPattern';
my $backtranslate = $pattern_obj->backtranslate;
isa_ok $backtranslate, 'Bio::Tools::SeqPattern';
is $backtranslate->str, $line->[1],
}
}
__DATA__
MAEELKAVAP ATGGCNGARGARYTNAARGCNGTNGCNCCN
LKGHB[WhYq]Q YTNAARGGNCAYRAYYRNCAR
(LK){2,3}[^GHB][WHYQ]Q (YTNAAR){2,3}HBNYRNCAR
LK[^GHB][WHYQ]Q YTNAARHBNYRNCAR
(LK){2,3}[^GHB][WHYQ]QX.X (YTNAAR){2,3}HBNYRNCARNNNNNNNNN
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