[Bioperl-l] Base symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC

[Conrad Halling]

Quick summary:

'X' is recognized as a valid base symbol by Bio::Tools::IUPAC but not by 
Bio::Restriction::Enzyme. Should 'X' be removed from Bio::Tools::IUPAC 
or should it be added to Bio::Restriction::Enzyme?

Detailed explanation:

I tried to use the Bio::Restriction modules to perform a simple 
restriction analysis of some sequences I'm using at work, and I found 
the documentation and code confusing. So I'm volunteering to overhaul 
and redocument these modules. As part of this effort, I am also 
volunteering to fix the Bio::Restriction::IO::bairoch module.

I have begun writing a test suite, RestrictionEnzyme.t, for the 
Bio::Restriction::Enzyme module. For one of the tests, I created a 
Bio::Restriction::Enzyme object with a recognition sequence that 
includes all of the IUPAC base symbols along with the caret ('^') 
symbol. A code excerpt is:

use Bio::Tools::IUPAC;
my %iupac_iub = Bio::Tools::IUPAC::iupac_iub();
my $site = join( '', '^', sort( keys( %iupac_iub ) ) );
ok $enzyme =
    Bio::Restriction::Enzyme->new(
        -name   => 'IUPAC-IUB',
        -site   => $site );

This test fails because Bio::Tools::IUPAC module includes 'X' as a valid 
base symbol, whereas Bio::Restriction::Enzyme does not.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unrecognized characters in site: [^ABCDGHKMNRSTUVWXY]
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:359
STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:441
STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:337
STACK: t/RestrictionEnzyme.t:184
-----------------------------------------------------------

The symbols recognized by Bio::Restriction::Enzyme and Bio::Tools::IUPAC 
need to be synchronized. Since 'X' is not recommended by "Nomenclature 
for Incompletely Specified Bases in Nucleic Acid Sequences" (see 
http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html) (largely because it 
stands for xanthine), I am in favor of removing it as a valid symbol.

But I have a feeling that if 'X' is removed as a valid symbol from 
Bio::Tools::IUPAC, this will break a lot of existing code. So the 
simplest solution seems to be to add 'X' to the symbols recognized by 
Bio::Restriction::Enzyme.

Does anyone have a recommendation?

-- 
Conrad Halling
chhalling at verizon.net