[Bioperl-l] One to three letter code for amino acids

[Jason Stajich]

Somehow I really must have missed the discussion or let it slip out of
my head... I had added the method 'valid_aa' to CodonTable a little while
ago.  Should it be relocated to SeqUtils?

In addition, I want to do the following to allow us to centralize the
places where we keep the aa/nt codes.  Okay if I commit it?

% cvs diff Bio/Tools/CodonTable.pm
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/CodonTable.pm,v
retrieving revision 1.21
diff -r1.21 CodonTable.pm
168a169
> use Bio::Tools::IUPAC;
272,306c273,274
< my %iupac_dna =
<     ( 'a' => [qw( a       )],
<       'c' => [qw( c       )],
<       'g' => [qw( g       )],
<       't' => [qw( t       )],
<       'u' => [qw( t       )],
<       'm' => [qw( a c     )],
<       'r' => [qw( a g     )],
<       'w' => [qw( a t     )],
<       'k' => [qw( g t     )],
<       'y' => [qw( c t     )],
<       's' => [qw( c g     )],
<       'v' => [qw( a c g   )],
<       'h' => [qw( a c t   )],
<       'd' => [qw( a g t   )],
<       'b' => [qw( c g t   )],
<       'n' => [qw( a c g t )],
<       'x' => [qw( a c g t )],
<      );
<
< my %iupac_aa =
<     ( A => [qw(A)],      B => [qw(D N)],
<       C => [qw(C)],      D => [qw(D)],
<       E => [qw(E)],      F => [qw(F)],
<       G => [qw(G)],      H => [qw(H)],
<       I => [qw(I)],      K => [qw(K)],
<       L => [qw(L)],      M => [qw(M)],
<       N => [qw(N)],      P => [qw(P)],
<       Q => [qw(Q)],      R => [qw(R)],
<       S => [qw(S)],      T => [qw(T)],
<       U => [qw(U)],      V => [qw(V)],
<       W => [qw(W)],      X => [qw(X)],
<       Y => [qw(Y)],      Z => [qw(E Q)],
<       '*' => ['*']
<       );
---
> my %iupac_dna = Bio::Tools::IUPAC->iupac_iub();
> my %iupac_aa = Bio::Tools::IUPAC->iupac_iup();


On Wed, 12 Dec 2001, Kris Boulez wrote:

> Quoting Heikki Lehvaslaiho (heikki@ebi.ac.uk):
> > Kris,
> >
> > I brought this up a year or so ago. The consensus then was that we should
> > not overload current interfaces but instead collect these utility functions
> > in a separate place. I've put several, including this one, into
> > Bio::SeqUtils.
> >
> Sorry didn't look close enough.
>
> Kris,
> _______________________________________________
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> Bioperl-l@bioperl.org
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>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu