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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 84);
use_ok('Bio::Tools::CodonTable');
use_ok('Bio::CodonUsage::IO');
}
# create a table object by giving an ID
my $DEBUG = test_debug();
my $myCodonTable = Bio::Tools::CodonTable -> new ( -id => 16);
ok defined $myCodonTable;
isa_ok $myCodonTable, 'Bio::Tools::CodonTable';
# defaults to ID 1 "Standard"
$myCodonTable = Bio::Tools::CodonTable->new();
is $myCodonTable->id(), 1;
# invalid table should produce a warn and set default table (1)
my $stderr = '';
{
# capture stderr output
local *STDERR;
open STDERR, '>', \$stderr;
$myCodonTable->id(99);
}
like $stderr, qr/Not a valid codon table ID/;
is $myCodonTable->id, 1;
# change codon table
$myCodonTable->id(10);
is $myCodonTable->id, 10;
is $myCodonTable->name(), 'Euplotid Nuclear';
# enumerate tables as object method
my $table = $myCodonTable->tables();
cmp_ok (keys %{$table}, '>=', 19); # currently 19 known tables
is $table->{11}, 'Bacterial, Archaeal and Plant Plastid';
# enumerate tables as class method
$table = Bio::Tools::CodonTable->tables;
cmp_ok (values %{$table}, '>=', 19); # currently 19 known tables
is $table->{23}, 'Thraustochytrium Mitochondrial';
# translate codons
$myCodonTable->id(1);
eval {
$myCodonTable->translate();
};
ok ($@ =~ /EX/) ;
# Automatically completing translation of incomplete codons is no longer default
# behavior b/c of inconsistent behavior compared with Bio::PrimarySeq::translate
# and unexpected side effects (e.g. what if the last few bases isn't supposed to
# be translated). To re-establish this, pass a second argument to the method.
is $myCodonTable->translate(''), '';
my @ii = qw(ACT acu ATN gt ytr sar);
my @res = qw(T T X V L Z );
my $test = 1;
for my $i (0..$#ii) {
if ($res[$i] ne $myCodonTable->translate($ii[$i], 1) ) {
$test = 0;
print $ii[$i], ": |", $res[$i], "| ne |",
$myCodonTable->translate($ii[$i], 1), "|\n" if( $DEBUG);
last ;
}
}
ok ($test);
is $myCodonTable->translate('ag'), '';
is $myCodonTable->translate('ag',1), '';
is $myCodonTable->translate('jj'), '';
is $myCodonTable->translate('jj',1), '';
is $myCodonTable->translate('jjg'), 'X';
is $myCodonTable->translate('jjg',1), 'X';
is $myCodonTable->translate('gt'), '';
is $myCodonTable->translate('gt',1), 'V';
is $myCodonTable->translate('g'), '';
is $myCodonTable->translate('g',1), '';
# a more comprehensive test on ambiguous codes
my $seq = <<SEQ;
atgaaraayacmacracwackacyacsacvachacdacbacxagragyatmatwatyathcarcayc
cmccrccwcckccyccsccvcchccdccbccxcgmcgrcgwcgkcgycgscgvcghcgdcgbcgxctmctrct
wctkctyctsctvcthctdctbctxgargaygcmgcrgcwgckgcygcsgcvgchgcdgcbgcxggmggrggw
ggkggyggsggvgghggdggbggxgtmgtrgtwgtkgtygtsgtvgthgtdgtbgtxtartaytcmtcrtcwt
cktcytcstcvtchtcdtcbtcxtgyttrttytramgamggmgrracratrayytaytgytrsaasagsartaa;
SEQ
$seq =~ s/\s+//g;
@ii = grep { length == 3 } split /(.{3})/, $seq;
print join (' ', @ii), "\n" if( $DEBUG);
my $prot = <<PROT;
MKNTTTTTTTTTTTRSIIIIQHPPPPPPPPPPPRRRRRRRRRRRLLLLLLLLLLLEDAAAAAAAAAAAGGG
GGGGGGGGVVVVVVVVVVV*YSSSSSSSSSSSCLF*RRRBBBLLLZZZ*
PROT
$prot =~ s/\s//;
@res = split //, $prot;
print join (' ', @res), "\n" if( $DEBUG );
$test = 1;
for my $i (0..$#ii) {
if ($res[$i] ne $myCodonTable->translate($ii[$i]) ) {
$test = 0;
print $ii[$i], ": |", $res[$i], "| ne |",
$myCodonTable->translate($ii[$i]), "| @ $i\n" if( $DEBUG);
last ;
}
}
ok $test;
# reverse translate amino acids
is $myCodonTable->revtranslate('U'), 0;
is $myCodonTable->revtranslate('O'), 0;
is $myCodonTable->revtranslate('J'), 9;
is $myCodonTable->revtranslate('I'), 3;
my @RNA_codons = $myCodonTable->revtranslate('M', 'RNA');
is $RNA_codons[0], 'aug'; # test RNA output
@ii = qw(A l ACN Thr sER ter Glx);
@res = (
[qw(gct gcc gca gcg)],
[qw(ggc gga ggg act acc aca acg)],
[qw(tct tcc tca tcg agt agc)],
[qw(act acc aca acg)],
[qw(tct tcc tca tcg agt agc)],
[qw(taa tag tga)],
[qw(gaa gag caa cag)]
);
$test = 1;
TESTING: {
for my $i (0..$#ii) {
my @codonres = $myCodonTable->revtranslate($ii[$i]);
for my $j (0..$#codonres) {
if ($codonres[$j] ne $res[$i][$j]) {
$test = 0;
print $ii[$i], ': ', $codonres[$j], " ne ",
$res[$i][$j], "\n" if( $DEBUG);
last TESTING;
}
}
}
}
ok $test;
# boolean tests
$myCodonTable->id(1); # Standard table
ok $myCodonTable->is_start_codon('ATG'), 'is_start_codon, ATG';
is $myCodonTable->is_start_codon('GGH'), 0, 'is_start_codon, GGH';
ok $myCodonTable->is_start_codon('HTG'), 'is_start_codon, HTG';
is $myCodonTable->is_start_codon('CCC'), 0, 'is_start_codon, CCC';
ok $myCodonTable->is_ter_codon('UAG'), 'is_ter_codon, U should map to T, UAG';
ok $myCodonTable->is_ter_codon('TaG'), 'is_ter_codon,TaG';
ok $myCodonTable->is_ter_codon('TaR'), 'is_ter_codon,TaR';
ok $myCodonTable->is_ter_codon('tRa'), 'is_ter_codon,tRa';
is $myCodonTable->is_ter_codon('ttA'), 0, 'is_ter_codon,ttA';
# Ambiguous codons should fail
is $myCodonTable->is_ter_codon('NNN'), 0, 'is_ter_codon, ambiguous codons should fail, NNN';
is $myCodonTable->is_ter_codon('TAN'), 0, 'is_ter_codon, ambiguous codons should fail, TAN';
is $myCodonTable->is_ter_codon('CC'), 0, 'is_ter_codon, incomplete codons should fail, CC';
ok $myCodonTable->is_unknown_codon('jAG');
ok $myCodonTable->is_unknown_codon('jg');
is $myCodonTable->is_unknown_codon('UAG'), 0;
is $myCodonTable->translate_strict('ATG'), 'M';
#
# adding a custom codon table
#
my @custom_table =
( 'test1',
'FFLLSSSSYY**CC*WLLLL**PPHHQQR*RRIIIMT*TT*NKKSSRRV*VVAA*ADDEE*GGG'
);
ok my $custct = $myCodonTable->add_table(@custom_table);
is $custct, 32;
is $myCodonTable->translate('atgaaraayacmacracwacka'), 'MKNTTTT';
ok $myCodonTable->id($custct);
is $myCodonTable->translate('atgaaraayacmacracwacka'), 'MKXXTTT';
# test doing this via Bio::PrimarySeq object
use Bio::PrimarySeq;
ok $seq = Bio::PrimarySeq->new(-seq=>'atgaaraayacmacracwacka', -alphabet=>'dna');
is $seq->translate()->seq, 'MKNTTTT';
is $seq->translate(undef, undef, undef, undef, undef, undef, $myCodonTable)->seq, 'MKXXTTT';
# test gapped translated
ok $seq = Bio::PrimarySeq->new(-seq => 'atg---aar------aay',
-alphabet => 'dna');
is $seq->translate->seq, 'M-K--N';
ok $seq = Bio::PrimarySeq->new(-seq =>'ASDFGHKL');
is $myCodonTable->reverse_translate_all($seq), 'GCBWSNGAYTTYGGVCAYAARYTN';
ok $seq = Bio::PrimarySeq->new(-seq => 'ASXFHKL');
is $myCodonTable->reverse_translate_all($seq), 'GCBWSNNNNTTYCAYAARYTN';
#
# test reverse_translate_best(), requires a Bio::CodonUsage::Table object
#
ok $seq = Bio::PrimarySeq->new(-seq =>'ACDEFGHIKLMNPQRSTVWYX');
ok my $io = Bio::CodonUsage::IO->new(-file => test_input_file('MmCT'));
ok my $cut = $io->next_data();
is $myCodonTable->reverse_translate_best($seq,$cut), 'GCCTGCGACGAGTTCGGCCACATCAAGCTGATGAACCCCCAGCGCTCCACCGTGTGGTACNNN';
is $myCodonTable->reverse_translate_all($seq, $cut, 15), 'GCNTGYGAYGARTTYGGVCAYATYAARCTSATGAAYCCNCARMGVWSYACHGTSTGGTAYNNN';
#
# test 'Strict' table, requires a Bio::CodonUsage::Table object
#
$myCodonTable = Bio::Tools::CodonTable->new(); # Default Standard table
# boolean tests
is $myCodonTable->is_start_codon('ATG'), 1;
is $myCodonTable->is_start_codon('GTG'), 0;
is $myCodonTable->is_start_codon('TTG'), 1;
is $myCodonTable->is_start_codon('CTG'), 1;
is $myCodonTable->is_start_codon('CCC'), 0;
$myCodonTable->id(0); # Special 'Strict' table (ATG-only start)
is $myCodonTable->is_start_codon('ATG'), 1;
is $myCodonTable->is_start_codon('GTG'), 0;
is $myCodonTable->is_start_codon('TTG'), 0;
is $myCodonTable->is_start_codon('CTG'), 0;
is $myCodonTable->is_start_codon('CCC'), 0;
# Pterobranchia Mitochondrial codon table
$myCodonTable->id(24);
is $myCodonTable->is_start_codon('GTG'), 1;
is $myCodonTable->is_start_codon('CTG'), 1;
is $myCodonTable->translate_strict('TGA'), 'W';
# Candidate Division SR1 and Gracilibacteria codon table
$myCodonTable->id(25);
is $myCodonTable->is_start_codon('GTG'), 1;
is $myCodonTable->is_start_codon('CTG'), 0;
is $myCodonTable->translate_strict('TGA'), 'G';
|
