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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
##
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( $@ ) { use lib 't'; }
use Test;
plan tests => 28;
}
use Bio::PrimarySeq;
use Bio::Tools::SeqStats;
use vars ('$DEBUG');
my ($seqobj, $count, $seqobj_stats, $wt);
$seqobj = Bio::PrimarySeq->new(-seq=>'ACTGTGGCGTCAACTG',
-alphabet=>'dna', -id=>'test');
$seqobj_stats = Bio::Tools::SeqStats->new(-seq=>$seqobj);
ok defined($seqobj_stats) && ref($seqobj_stats) &&
$seqobj_stats->isa('Bio::Tools::SeqStats');
$count = $seqobj_stats->count_monomers(); # for DNA sequence
ok $count->{'A'}, 3;
ok $count->{'C'}, 4;
ok $count->{'G'}, 5;
ok $count->{'T'}, 4;
$count = $seqobj_stats->count_codons();
ok $count->{'ACT'}, 2;
ok $count->{'GTG'}, 1;
ok $count->{'GCG'}, 1;
ok $count->{'TCA'}, 1;
$seqobj = Bio::PrimarySeq->new(-seq=>'ACTACTTCA', -alphabet=>'dna',
-id=>'test');
$seqobj_stats = Bio::Tools::SeqStats->new('-seq' => $seqobj);
$wt = $seqobj_stats->get_mol_wt(); # for DNA sequence
ok $$wt[0], 2738 ;
$seqobj = Bio::PrimarySeq->new(-seq=>'ACXACNNCA',
-alphabet=>'dna', -id=>'test');
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
ok $$wt[0], 2693;
ok $$wt[1], 2813;
$seqobj = Bio::PrimarySeq->new(-seq=>'ACTGTGGCGTCAACTG',
-alphabet=>'dna', -id=>'test');
$count = Bio::Tools::SeqStats->count_monomers($seqobj); # for DNA sequence
ok $count->{'A'}, 3;
ok $count->{'C'}, 4;
ok $count->{'G'}, 5;
ok $count->{'T'}, 4;
$seqobj = Bio::PrimarySeq->new(-seq=>'MQSERGITIDISLWKFETSKYYVT',
-alphabet=>'protein', -id=>'test');
$seqobj_stats = Bio::Tools::SeqStats->new('-seq' => $seqobj);
$count = $seqobj_stats->count_monomers(); # for amino sequence
ok $$count{'M'}, 1;
ok $$count{'I'}, 3;
ok $$count{'Y'}, 2;
ok $$count{'T'}, 3;
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
ok $$wt[0], 2896;
ok $$wt[1], 2896;
$seqobj = Bio::PrimarySeq->new(-seq=>'UYXUYNNYU', -alphabet=>'rna');
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
ok $$wt[0], 2768;
ok $$wt[1], 2891;
ok $seqobj = Bio::PrimarySeq->new(-seq=>'TGCCGTGTGTGCTGCTGCT', -alphabet=>'rna');
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
ok $$wt[0], 6104 ;
# selenocysteine
ok $seqobj = Bio::PrimarySeq->new(-seq=>'MQSERGITIDISLWKFETSKYYVT',
-alphabet=>'protein');
$wt = Bio::Tools::SeqStats->get_mol_wt($seqobj);
ok $$wt[0], 2896 ;
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