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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 46);
use_ok('Bio::Tools::IUPAC');
use_ok('Bio::Seq');
use_ok('Bio::PrimarySeq');
}
# IUPAC sequences and regular expressions
my $ambiseq = Bio::Seq->new(
-seq => 'ARTCGTTGN',
-alphabet => 'dna',
);
my $ambiprimaryseq = Bio::Seq->new(
-seq => 'ARTCGTTGN',
-alphabet => 'dna',
);
ok my $iupac = Bio::Tools::IUPAC->new( -seq => $ambiprimaryseq );
ok $iupac = Bio::Tools::IUPAC->new( -seq => $ambiseq );
ok my $regexp = $iupac->regexp, 'Regexp';
is $regexp, 'A[AGR]TCGTTG[ACGTBDHKMNRSVWY]';
$regexp = $iupac->regexp(1);
is $regexp, 'A[AGR][TU]CG[TU][TU]G[ACGTUBDHKMNRSVWY]', 'Regexp';
is $iupac->count(), 8, 'Count';
my @seqs;
while (my $uniqueseq = $iupac->next_seq()) {
push @seqs, $uniqueseq->seq;
is $uniqueseq->isa('Bio::PrimarySeqI'), 1;
like $uniqueseq->seq, qr/$regexp/i;
}
@seqs = sort @seqs;
is_deeply \@seqs, [ 'AATCGTTGA', 'AATCGTTGC', 'AATCGTTGG', 'AATCGTTGT',
'AGTCGTTGA', 'AGTCGTTGC', 'AGTCGTTGG', 'AGTCGTTGT' ];
like $ambiseq->seq, qr/$regexp/i, 'Regexp matches ambiguous sequences';
like 'ARTCGTTGW', qr/$regexp/i;
# IUPAC code methods
my %iupac;
ok %iupac = $iupac->iupac_iub(), 'Nucleic IUPAC';
ok exists $iupac{'A'};
ok not exists $iupac{'Z'};
ok %iupac = $iupac->iupac_iub_amb();
ok exists $iupac{'N'};
ok not exists $iupac{'A'};
ok %iupac = $iupac->iupac_rev_iub();
ok %iupac = $iupac->iupac_iup(), 'Proteic IUPAC';
ok exists $iupac{'A'};
ok exists $iupac{'Z'};
ok %iupac = $iupac->iupac_iup_amb();
ok exists $iupac{'B'};
ok not exists $iupac{'A'};
ok %iupac = $iupac->iupac();
ok not(exists $iupac{'Z'});
ok %iupac = $iupac->iupac_amb();
ok not(exists $iupac{'A'});
ok %iupac = Bio::Tools::IUPAC->new->iupac_iup;
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