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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: Seq.t,v 1.23 2002/01/06 18:50:51 birney 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 => 38;
}
use Bio::Seq;
use Bio::Seq::RichSeq;
use Bio::SeqFeature::Generic;
use Bio::Annotation;
use Bio::Species;
ok(1);
my $seq = Bio::Seq->new(-seq=>'ACTGTGGCGTCAACT',
-desc=>'Sample Bio::Seq object',
-alphabet => 'dna' );
ok $seq;
my $trunc = $seq->trunc(1,4);
ok $trunc->length, 4, 'truncated sequence was not of length 4';
ok $trunc->seq, 'ACTG', 'truncated sequence was not ACTG instead was '. $trunc->seq();
# test ability to get str function
ok $seq->seq(), 'ACTGTGGCGTCAACT' ;
ok $seq = Bio::Seq->new(-seq=>'actgtggcgtcaact',
-desc=>'Sample Bio::Seq object',
-display_id => 'something',
-accession_number => 'accnum',
-alphabet => 'dna' );
ok uc $seq->alphabet, 'DNA' , 'alphabet was ' .$seq->alphabet();
# basic methods
ok $seq->id(), 'something', "saw ".$seq->id;
ok $seq->accession_number, 'accnum', "saw ". $seq->accession_number ;
ok $seq->subseq(5, 9), 'tggcg', "subseq(5,9) was ". $seq->subseq(5,9);
my $newfeat = Bio::SeqFeature::Generic->new( -start => 10,
-end => 12,
-primary => 'silly',
-source => 'stuff');
$seq->add_SeqFeature($newfeat);
ok $seq->feature_count, 1;
my $species = new Bio::Species
(-verbose => 1,
-classification => [ qw( sapiens Homo Hominidae
Catarrhini Primates Eutheria
Mammalia Vertebrata Chordata
Metazoa Eukaryota )]);
$seq->species($species);
ok $seq->species->binomial, 'Homo sapiens';
$seq->annotation(new Bio::Annotation('-description' => 'desc-here'));
ok $seq->annotation->description, 'desc-here',
'annotation was ' . $seq->annotation();
#
# translation tests
#
my $trans = $seq->translate();
ok $trans->seq(), 'TVAST' , 'translated sequence was ' . $trans->seq();
# unambiguous two character codons like 'ACN' and 'GTN' should give out an amino acid
$seq->seq('ACTGTGGCGTCAAC');
$trans = $seq->translate();
ok $trans->seq(), 'TVAST', 'translated sequence was ' . $trans->seq();
$seq->seq('ACTGTGGCGTCAACA');
$trans = $seq->translate();
ok $trans->seq(), 'TVAST', 'translated sequence was ' . $trans->seq();
$seq->seq('ACTGTGGCGTCAACAG');
$trans = $seq->translate();
ok $trans->seq(), 'TVAST', 'translated sequence was ' . $trans->seq();
$seq->seq('ACTGTGGCGTCAACAGT');
$trans = $seq->translate();
ok $trans->seq(), 'TVASTV', 'translated sequence was ' . $trans->seq();
$seq->seq('ACTGTGGCGTCAACAGTA');
$trans = $seq->translate();
ok $trans->seq(), 'TVASTV', 'translated sequence was ' . $trans->seq();
$seq->seq('AC');
ok $seq->translate->seq , 'T', 'translated sequence was ' . $seq->translate->seq();
#difference between the default and full CDS translation
$seq->seq('atgtggtaa');
$trans = $seq->translate();
ok $trans->seq(), 'MW*' , 'translated sequence was ' . $trans->seq();
$seq->seq('atgtggtaa');
$trans = $seq->translate(undef,undef,undef,undef,1);
ok $trans->seq(), 'MW', 'translated sequence was ' . $trans->seq();
#frame
my $string;
my @frames = (0, 1, 2);
foreach my $frame (@frames) {
$string .= $seq->translate(undef, undef, $frame)->seq;
$string .= $seq->revcom->translate(undef, undef, $frame)->seq;
}
ok $string, 'MW*LPHCGYHVVTT';
#Translating with all codon tables using method defaults
$string = '';
my @codontables = qw( 1 2 3 4 5 6 9 10 11 12 13 14 15 16 21 22 23);
foreach my $ct (@codontables) {
$string .= $seq->translate(undef, undef, undef, $ct)->seq;
}
ok $string, 'MW*MW*MW*MW*MW*MWQMW*MW*MW*MW*MW*MWYMW*MW*MW*MW*MW*';
# CDS translation set to throw an exception for internal stop codons
$seq->seq('atgtggtaataa');
eval {
$seq->translate(undef, undef, undef, undef, 'CDS' , 'throw');
};
ok ($@ =~ /EX/) ;
$seq->seq('atgtggtaataa');
ok( $seq->translate('J', '-',)->seq, 'MWJJ');
# tests for RichSeq
my $richseq = Bio::Seq::RichSeq->new( -seq => 'atgtggtaataa',
-accession_number => 'AC123',
-alphabet => 'rna',
-molecule => 'mRNA',
-id => 'id1',
-dates => [ '2001/1/1' ],
-pid => '887821',
-keywords => 'JUNK1 JUNK2',
-division => 'Fungi',
-secondary_accessions => 'AC1152' );
ok ($richseq);
ok ($richseq->seq, 'atgtggtaataa');
ok ($richseq->display_id, 'id1');
ok (($richseq->get_dates)[0], '2001/1/1');
ok (($richseq->get_secondary_accessions)[0], 'AC1152');
ok ($richseq->accession_number, 'AC123');
ok ($richseq->alphabet, 'rna');
ok ($richseq->molecule, 'mRNA');
ok ($richseq->pid, 887821);
ok ($richseq->division, 'Fungi');
ok ($richseq->keywords, 'JUNK1 JUNK2');
$richseq->seq_version('2');
ok ($richseq->seq_version, 2);
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