[Bioperl-guts-l] bioperl-live/Bio SeqUtils.pm,1.33,1.34

[Christopher John Fields]

Update of /home/repository/bioperl/bioperl-live/Bio
In directory dev.open-bio.org:/tmp/cvs-serv25795/Bio

Modified Files:
	SeqUtils.pm 
Log Message:
Added additional IUPAC amino acids GenBank is adding starting in October (per Neil Saunders on the mail list)

Index: SeqUtils.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqUtils.pm,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** SeqUtils.pm	27 Jul 2006 00:04:37 -0000	1.33
--- SeqUtils.pm	15 Aug 2006 04:59:01 -0000	1.34
***************
*** 122,126 ****
  
  BEGIN {
! 
      %ONECODE =
      ('Ala' => 'A', 'Asx' => 'B', 'Cys' => 'C', 'Asp' => 'D',
--- 122,126 ----
  
  BEGIN {
!     # Note : Ambiguity code 'J' = I/L (used for ambiguities in mass-spec data)
      %ONECODE =
      ('Ala' => 'A', 'Asx' => 'B', 'Cys' => 'C', 'Asp' => 'D',
***************
*** 130,134 ****
       'Ser' => 'S', 'Thr' => 'T', 'Val' => 'V', 'Trp' => 'W',
       'Xaa' => 'X', 'Tyr' => 'Y', 'Glx' => 'Z', 'Ter' => '*',
!      'Sec' => 'U'
       );
  
--- 130,134 ----
       'Ser' => 'S', 'Thr' => 'T', 'Val' => 'V', 'Trp' => 'W',
       'Xaa' => 'X', 'Tyr' => 'Y', 'Glx' => 'Z', 'Ter' => '*',
!      'Sec' => 'U', 'Pyl' => 'O', 'Xle' => 'J'
       );
  
***************
*** 140,144 ****
       'S' => 'Ser', 'T' => 'Thr', 'V' => 'Val', 'W' => 'Trp',
       'Y' => 'Tyr', 'Z' => 'Glx', 'X' => 'Xaa', '*' => 'Ter',
!      'U' => 'Sec'
       );
  }
--- 140,144 ----
       'S' => 'Ser', 'T' => 'Thr', 'V' => 'Val', 'W' => 'Trp',
       'Y' => 'Tyr', 'Z' => 'Glx', 'X' => 'Xaa', '*' => 'Ter',
!      'U' => 'Sec', 'O' => 'Pyl', 'J' => 'Xle'
       );
  }