3 :>"^Å ã@sêdZddlmZddlmZejejjƒks0t‚Gdd„dejƒZ e ƒZ ej ej jƒks\t‚Gdd„de ƒZ e ƒZ Gdd „d ejƒZeƒZGd d „d eƒZeƒZGd d „d ejƒZeƒZGdd„dejƒZeƒZGdd„deƒZeƒZdS)z;Standard nucleotide and protein alphabets defined by IUPAC.é)ÚAlphabet)Ú IUPACDatac@seZdZdZejZdS)ÚExtendedIUPACProteinalExtended 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). N)Ú__name__Ú __module__Ú __qualname__Ú__doc__rÚextended_protein_lettersÚletters©r r úb/home/psgendb/BIRCHDEV/lib-linux-x86_64/python/lib64/python3.5/site-packages/Bio/Alphabet/IUPAC.pyrsrc@seZdZdZejZdS)Ú IUPACProteinz]IUPAC protein alphabet of the 20 standard amino acids. Uppercase and single letter. N)rrrrrÚprotein_lettersr r r r r r /sr c@seZdZdZejZdS)ÚIUPACAmbiguousDNAzUppercase IUPAC ambiguous DNA.N)rrrrrZambiguous_dna_lettersr r r r r r?src@seZdZdZejZdS)ÚIUPACUnambiguousDNAz4Uppercase IUPAC unambiguous DNA (letters GATC only).N)rrrrrÚunambiguous_dna_lettersr r r r r rHsrc@seZdZdZejZdS)ÚExtendedIUPACDNAzÔExtended IUPAC DNA alphabet. In addition to the standard letter codes GATC, this includes: - ``B`` = 5-bromouridine - ``D`` = 5,6-dihydrouridine - ``S`` = thiouridine - ``W`` = wyosine N)rrrrrZextended_dna_lettersr r r r r rRs rc@seZdZdZejZdS)ÚIUPACAmbiguousRNAzUppercase IUPAC ambiguous RNA.N)rrrrrZambiguous_rna_lettersr r r r r rfsrc@seZdZdZejZdS)ÚIUPACUnambiguousRNAz4Uppercase IUPAC unambiguous RNA (letters GAUC only).N)rrrrrÚunambiguous_rna_lettersr r r r r rosrN)rÚBiorÚBio.Datarr ÚupperÚAssertionErrorÚProteinAlphabetrZextended_proteinrr ÚproteinÚ DNAAlphabetrZ ambiguous_dnarZunambiguous_dnarZ extended_dnaÚ RNAAlphabetrZ ambiguous_rnarZunambiguous_rnar r r r Ús&