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Bug in is_ter_codon #387

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Bug in is_ter_codon #387

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120a20a
is_ter_codon and is_start_codon do not behaves thesame. Now it does. …
Juke34 Feb 16, 2024
d3ae01e
add ambiguous codons tests for is_start_codon and modify ambiguous co…
Juke34 Feb 21, 2024
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29 changes: 3 additions & 26 deletions lib/Bio/Tools/CodonTable.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -735,41 +735,18 @@ sub is_start_codon{
=head2 is_ter_codon

Title : is_ter_codon
Usage : $obj->is_ter_codon('GAA')
Usage : $obj->is_ter_codon('TGA')
Function: returns true (1) for all codons that can be used as a
translation tarminator, false (0) for others.
Example : $myCodonTable->is_ter_codon('ATG')
Example : $myCodonTable->is_ter_codon('TGA')
Returns : boolean
Args : codon

=cut

sub is_ter_codon{
my ($self, $value) = @_;
my $id = $self->{'id'};

# We need to ensure U is mapped to T (ie. UAG)
$value = uc $value;
$value =~ tr/U/T/;

if (length $value != 3 ) {
# Incomplete codons are not stop codons
return 0;
} else {
my $result = 0;

# For all the possible codons, if any are not a stop
# codon, fail immediately
for my $c ( $self->unambiguous_codons($value) ) {
my $m = substr( $TABLES[$id], $CODONS->{$c}, 1 );
if($m eq $TERMINATOR) {
$result = 1;
} else {
return 0;
}
}
return $result;
}
shift->_codon_is( shift, \@STARTS, '*' );
}

# desc: compares the passed value with a single entry in the given
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12 changes: 8 additions & 4 deletions t/SeqTools/CodonTable.t
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ use strict;
BEGIN {
use Bio::Root::Test;

test_begin(-tests => 84);
test_begin(-tests => 87);

use_ok('Bio::Tools::CodonTable');
use_ok('Bio::CodonUsage::IO');
Expand Down Expand Up @@ -170,9 +170,13 @@ 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';
# Ambiguous codons
is $myCodonTable->is_start_codon('NNN'), 1, 'is_start_codon, ambiguous codons should succeed, NNN';
is $myCodonTable->is_start_codon('ATN'), 1, 'is_start_codon, ambiguous codons should succeed, ATN';
is $myCodonTable->is_start_codon('CC'), 0, 'is_ter_codon, incomplete codons should fail, CC';

is $myCodonTable->is_ter_codon('NNN'), 1, 'is_ter_codon, ambiguous codons should succeed, NNN';
is $myCodonTable->is_ter_codon('TAN'), 1, 'is_ter_codon, ambiguous codons should succeed, TAN';
is $myCodonTable->is_ter_codon('CC'), 0, 'is_ter_codon, incomplete codons should fail, CC';

ok $myCodonTable->is_unknown_codon('jAG');
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