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#-*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: CodonTable.t,v 1.14 2002/01/06 18:50:51 birney Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
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( $@ ) {
use lib 't';
}
use Test;
plan tests => 30;
}
use Bio::Tools::CodonTable;
use vars qw($DEBUG);
ok(1);
# create a table object by giving an ID
$DEBUG = 0;
my $myCodonTable = Bio::Tools::CodonTable -> new ( -id => 16);
ok defined $myCodonTable;
ok $myCodonTable->isa('Bio::Tools::CodonTable');
# defaults to ID 1 "Standard"
$myCodonTable = Bio::Tools::CodonTable->new();
ok $myCodonTable->id(), 1;
# change codon table
$myCodonTable->id(10);
ok $myCodonTable->id, 10;
ok $myCodonTable->name(), 'Euplotid Nuclear';
# translate codons
$myCodonTable->id(1);
eval {
$myCodonTable->translate();
};
ok ($@ =~ /EX/) ;
ok $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]) ) {
$test = 0;
print $ii[$i], ": |", $res[$i], "| ne |", $myCodonTable->translate($ii[$i]), "|\n" if( $DEBUG);
last ;
}
}
ok ($test);
ok $myCodonTable->translate('ag'), '';
ok $myCodonTable->translate('jj'), '';
ok $myCodonTable->translate('jjg'), 'X';
ok $myCodonTable->translate('gt'), 'V';
ok $myCodonTable->translate('g'), '';
# 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
ok $myCodonTable->revtranslate('J'), 0;
@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);
ok $myCodonTable->is_start_codon('ATG');
ok( $myCodonTable->is_start_codon('GGH'), 0);
ok $myCodonTable->is_start_codon('HTG');
ok $myCodonTable->is_start_codon('CCC'), 0;
ok $myCodonTable->is_ter_codon('UAG');
ok $myCodonTable->is_ter_codon('TaG');
ok $myCodonTable->is_ter_codon('TaR');
ok $myCodonTable->is_ter_codon('tRa');
ok $myCodonTable->is_ter_codon('ttA'), 0;
ok $myCodonTable->is_unknown_codon('jAG');
ok $myCodonTable->is_unknown_codon('jg');
ok $myCodonTable->is_unknown_codon('UAG'), 0;
ok $myCodonTable->translate_strict('ATG'), 'M';
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