ó
h<Ic           @   s¿  d  Z  d d l m Z d d l m Z e j e j j ƒ  k sD t ‚ d e j f d „  ƒ  YZ	 e	 ƒ  Z
 e j e j j ƒ  k s„ t ‚ d e	 f d „  ƒ  YZ e ƒ  Z d e j f d	 „  ƒ  YZ e ƒ  Z d
 e f d „  ƒ  YZ e ƒ  Z d e j f d „  ƒ  YZ e ƒ  Z d e j f d „  ƒ  YZ e ƒ  Z d e f d „  ƒ  YZ e ƒ  Z d d l m Z d „  Z e e j e <e e j e	 <e e j e <e e j e <e e j e <e e j e <e e j e <d S(   s;   Standard nucleotide and protein alphabets defined by IUPAC.iÿÿÿÿ(   t   Alphabet(   t	   IUPACDatat   ExtendedIUPACProteinc           B   s   e  Z d  Z e j Z RS(   sD  Extended uppercase IUPAC protein single letter alphabet including X etc.

    In addition to the standard 20 single letter protein codes, this includes:
    
    B = "Asx";  Aspartic acid (R) or Asparagine (N)
    X = "Xxx";  Unknown or 'other' amino acid
    Z = "Glx";  Glutamic acid (E) or Glutamine (Q)
    J = "Xle";  Leucine (L) or Isoleucine (I), used in mass-spec (NMR)
    U = "Sec";  Selenocysteine
    O = "Pyl";  Pyrrolysine

    This alphabet is not intended to be used with X for Selenocysteine
    (an ad-hoc standard prior to the IUPAC adoption of U instead).
    (   t   __name__t
   __module__t   __doc__R   t   extended_protein_letterst   letters(    (    (    s…   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Alphabet/IUPAC.pyR      s   t   IUPACProteinc           B   s   e  Z d  Z e j Z RS(   sN   Uppercase IUPAC protein single letter alphabet of the 20 standard amino acids.(   R   R   R   R   t   protein_lettersR   (    (    (    s…   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Alphabet/IUPAC.pyR   '   s   t   IUPACAmbiguousDNAc           B   s   e  Z d  Z e j Z RS(   s   Uppercase IUPAC ambiguous DNA.(   R   R   R   R   t   ambiguous_dna_lettersR   (    (    (    s…   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Alphabet/IUPAC.pyR
   1   s   t   IUPACUnambiguousDNAc           B   s   e  Z d  Z e j Z RS(   s4   Uppercase IUPAC unambiguous DNA (letters GATC only).(   R   R   R   R   t   unambiguous_dna_lettersR   (    (    (    s…   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Alphabet/IUPAC.pyR   7   s   t   ExtendedIUPACDNAc           B   s   e  Z d  Z e j Z RS(   s»   Extended IUPAC DNA alphabet.

    In addition to the standard letter codes GATC, this includes:

    B = 5-bromouridine
    D = 5,6-dihydrouridine
    S = thiouridine
    W = wyosine
    (   R   R   R   R   t   extended_dna_lettersR   (    (    (    s…   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Alphabet/IUPAC.pyR   ?   s   	t   IUPACAmbiguousRNAc           B   s   e  Z d  Z e j Z RS(   s   Uppercase IUPAC ambiguous RNA.(   R   R   R   R   t   ambiguous_rna_lettersR   (    (    (    s…   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Alphabet/IUPAC.pyR   O   s   t   IUPACUnambiguousRNAc           B   s   e  Z d  Z e j Z RS(   s4   Uppercase IUPAC unambiguous RNA (letters GAUC only).(   R   R   R   R   t   unambiguous_rna_lettersR   (    (    (    s…   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Alphabet/IUPAC.pyR   U   s   (   t   default_managerc         C   sx   |  t  k s t ‚ t  j t =t  j t =t  j t =t  j t =t  j t =t  j t =t  j t	 =d d l
 m } |  j | | ƒ S(   Niÿÿÿÿ(   t   IUPACEncoding(   R   t   AssertionErrort   class_resolverR   R   R
   R   R   R   R   t   Bio.EncodingsR   t   resolve_class(   t   managert   klasst   propertyR   (    (    s…   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Alphabet/IUPAC.pyt
   _bootstrapk   s    






N(   R   t   BioR    t   Bio.DataR   R   t   upperR   t   ProteinAlphabetR   t   extended_proteinR	   R   t   proteint   DNAAlphabetR
   t   ambiguous_dnaR   t   unambiguous_dnaR   t   extended_dnat   RNAAlphabetR   t   ambiguous_rnaR   t   unambiguous_rnat   Bio.PropertyManagerR   R   R   (    (    (    s…   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Alphabet/IUPAC.pyt   <module>   s6   								