XfV*dZddlmZddlmZiZiZiZiZiZ iZ iZ iZ iZ iZiZiZdadaGddeZGddZd ZGd d eZGd d eZGddeZGddeZdZdZeddgejgdksJeddgejddgksJeddgejgdksJeddgejgdksJegdejgdksJGddZd Z e d!d"d#id$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3d5d6d7d(d8d(d9d(d:d(id;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPdQdRidSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdgdfdfdfdhdhdididjdjdjdjdk gdlgdmne dodpdqid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3dd6d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdPdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d`dadbdadcdadddadedfdgdfdrdfdfdhdhdididjdjdjdjds gdtgdune dvdwdxid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3dd6d5d6d7dRd8dRd9dRid:dRd;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdPdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddggdzne d{d|d}id$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3dd6d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddggd~ne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3dd6d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdPdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^d+d_d+d`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddggdne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0ddDddDd2d3d4d3d5d6d7d(d8d(id9d(d:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLidOdPdQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadfdfdfdfdhdhdididjdjdjdjd dgdOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3dd6d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdWd[dZd\d+d]d+d^d+d_d+d`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddgdOddgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3dd3d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddgdOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3d5d6d7d(d8d(d9d(d:d(id;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPdQdRidSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdgdfdfdfdhdhdididjdjdjdjdk gdlgdne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3d5d6d7d(d8d(d9d(d:d+id;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPdQdRidSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdgdfdfdfdhdhdididjdjdjdjdk gdld:dOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3dd6d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdPdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^djd_djd`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddggdne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0dd0d2d3d4d3dd6d5d6d7d(d8d(id9d(d:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLidOdPdQdRdSdRdTdRdUdRdVdWdXdWdYdWd[dZd\d+d]d+d^d+d_d+d`dadbdadcdadddadfdfdfdfdhdhdididjdjdjdjd dgdOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0ddDd2d3d4d3d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddgdOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0dd(d2d3d4d3d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddgdOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3dd6d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdPdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdWd[dZd\d+d]d+d^d+d_d+d`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddgdOddgne dddid$d%d&d%d'd(d)d(d*d+d,d+d.d+d/d0d1d0dd(d2d3d4d3d5d6d7d(d8d(d9d(d:d(id;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPdQdRidSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdgdfdfdfdhdhdididjdjdjdjdk gddOgne dddid$d%d&d%d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3d5d6d7d(d8d(d9d(d:d(d;d<id=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPdQdRdSdRidTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdgdfdrdfdfdhdhdididjdjdjdjds gdgdne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3dd6d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^d+d_dZd`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddggdne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3ddjd5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddggdne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0d2d3d4d3d5d6d7d(d8d(d9d(d:dfid;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPdQdRidSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdgdfdfdfdhdhdididjdjdjdjdk gdld:dOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0ddDddDd2d3d4d3dd6d5d6d7d(id8d(d9d(d:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLidNdLdOdPdQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadadfdfdfdfdhdhdididjdjdjdjd dgdOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0ddDddDd2d3d4d3dd6d5d6d7d(id8d(d9d(d:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLidNdLdOdPdQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadadfdfdfdfdhdhdididjdjdjdjd gdldOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0dd0dd0d2d3d4d3d5d6d7d(d8d(id9d(d:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLidOdPdQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadfdfdfdfdhdhdididjdjdjdjd dgdOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0ddiddid2d3d4d3d5d6d7d(d8d(id9d(d:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLidOdPdQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadfdfdfdfdhdhdididjdjdjdjd dgdOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0ddiddid2d3d4d3dd6d5d6d7d(id8d(d9d(d:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLidNdLdOdPdQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadadfdfdfdfdhdhdididjdjdjdjd ddgdOgne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0dd6d2d3d4d3d5d6d7d(d8d(d9d(id:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLdOdPidQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^dGd_dGd`dadbdadcdadddadedfdfdfdfdhdhdididjdjdjdjdy ddggdne dddid$d%d&d%d'd(d)d(d*d+d,d+d-d+d.d+d/d0d1d0dd0d2d3d4d3dd6d5d6d7d(d8d(id9d(d:d(d;d<d=d<d>d<d?d<d@dAdBdAdCdDdEdDdFdGdHdGdIdGdJdGdKdLdMdLdNdLidOdPdQdRdSdRdTdRdUdRdVdWdXdWdYdZd[dZd\d+d]d+d^d+d_dZd`dadbdadcdadddadfdfdfdfdhdhdididjdjdjdjd dggdndS)zCodon tables based on those from the NCBI. These tables are based on parsing the NCBI file ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt using Scripts/update_ncbi_codon_table.py Last updated at Version 4.4 (May 2019) )Optional) IUPACDataNceZdZdZdS)TranslationErrorz.Container for translation specific exceptions.N)__name__ __module__ __qualname____doc__3lib/python3.11/site-packages/Bio/Data/CodonTable.pyrr,s8888r rc eZdZUdZiZeeefed<iZeeefed<gZ e eed<gZ e eed<ddeee e fde ede edeeefdeeefde ede ed dfd Z d ZdS) CodonTablezA codon-table, or genetic code. forward_table back_table start_codons stop_codonsNnucleotide_alphabetprotein_alphabetreturncZ||_||_||_||_||_||_dSInitialize the class.N)rrrrrr)selfrrrrrrs r __init__zCodonTable.__init__9s9$7 0*$(&r c|jr d|jz}nd}|jr*|ddd|jDzz }|j}|d|vrd}nd }|d z }|d d d |Dzd zz }|ddd|Dzdzz }|D]}|D]}|dz}|D]k}||z|z}|d|z }||jvr|dz }! |j|}n#t $rd}Ynt$rd}YnwxYw||jvr |d|dz }b|d|dz }l|d|zz }|d|zz }|ddd|Dzdzz }|S)aReturn a simple text representation of the codon table. e.g.:: >>> import Bio.Data.CodonTable >>> print(Bio.Data.CodonTable.standard_dna_table) Table 1 Standard, SGC0 | T | C | A | G | --+---------+---------+---------+---------+-- T | TTT F | TCT S | TAT Y | TGT C | T T | TTC F | TCC S | TAC Y | TGC C | C ... G | GTA V | GCA A | GAA E | GGA G | A G | GTG V | GCG A | GAG E | GGG G | G --+---------+---------+---------+---------+-- >>> print(Bio.Data.CodonTable.generic_by_id[1]) Table 1 Standard, SGC0 | U | C | A | G | --+---------+---------+---------+---------+-- U | UUU F | UCU S | UAU Y | UGU C | U U | UUC F | UCC S | UAC Y | UGC C | C ... G | GUA V | GCA A | GAA E | GGA G | A G | GUG V | GCG A | GAG E | GGG G | G --+---------+---------+---------+---------+-- zTable %izTable ID unknown , cg|]}||Sr r .0xs r z&CodonTable.__str__..ls&B&B&BQ&Bq&B&B&Br NTTCAGUCAGz z ||c3"K|] }d|dV dS)z z Nr r!c2s r z%CodonTable.__str__..zs*"E"Er????"E"E"E"E"E"Er z --++c3K|]}dVdSz ---------Nr r)s r r+z%CodonTable.__str__..{s"$C$CR[$C$C$C$C$C$Cr z+--z |z Stop|?z(s)|z | c3K|]}dVdSr.r r)s r r+z%CodonTable.__str__..s"(G(G(G(G(G(G(G(Gr ) idnamesjoinrrrKeyErrorrr) ranswerlettersc1c3liner*codonaminos r __str__zCodonTable.__str__Js4: 7 ($')FF'F : D cDII&B&B$*&B&B&BCCC CF*  3'>>GGG &%#(("E"EW"E"E"EEEEKK'CHH$C$C7$C$C$CCCCeKK P PB & &Dy!44BGbLEKKK'D 000(($($6u$=EE'((($'EEE/((($'EEE( D$555 OOOO3DD OOOO3DDb $+% g(G(Gw(G(G(G G GG%O OFF s C,, D : D D )rrr r rdictstr__annotations__rrlistrrrr=r r r rr0s))$&M4S>&&&!#JS#X### L$s)   Kc .2*.(5%/".!,''%c]'#3-'CH~ ' cN ' 3i '#Y' ''''"HHHHHr rcNi}t|D] }||||<||d<|S)zBack a back-table (naive single codon mapping). ONLY RETURNS A SINGLE CODON, chosen from the possible alternatives based on their sort order. N)sorted)tabledefault_stop_codonrkeys r make_back_tablerGs?Je}}%%!$ 5:)Jt r cHeZdZUdZdZeeed<ej Z dZ dZ dS)NCBICodonTablez-Codon table for generic nucleotide sequences.Nrc||_||_||_t||d|_||_||_dS)rrN)r2r3rrGrrr)rr2r3rDrrs r rzNCBICodonTable.__init__sC ")%Q@@(&r c@|jjd|jd|jdS)z?Represent the NCBI codon table class as a string for debugging.z(id=z, names=z, ...)) __class__rr2r3)rs r __repr__zNCBICodonTable.__repr__s*.)VVtwVV$*VVVVr ) rrr r rrr?r@rprotein_lettersrrrMr r r rIrIs]77)-#--- 0'''WWWWWr rIc eZdZdZejZdS)NCBICodonTableDNAz*Codon table for unambiguous DNA sequences.N)rrr r runambiguous_dna_lettersrr r r rPrP44#;r rPc eZdZdZejZdS)NCBICodonTableRNAz*Codon table for unambiguous RNA sequences.N)rrr r runambiguous_rna_lettersrr r r rTrTrRr rTceZdZdZdZdZdS)AmbiguousCodonTablez)Base codon table for ambiguous sequences.c t|||t|j|||jt |j|t |j|||_dSr) rrAmbiguousForwardTablerrlist_ambiguous_codonsrr _codon_table)r codon_tableambiguous_nucleotide_alphabetambiguous_nucleotide_valuesambiguous_protein_alphabetambiguous_protein_valuess r rzAmbiguousCodonTable.__init__s   ) & !)+(    " "(*E   "+"9;V W W!   $(r c,t|j|S)z0Forward attribute lookups to the original table.)getattrr[)rnames r __getattr__zAmbiguousCodonTable.__getattr__st($///r N)rrr r rrdr r r rWrWs933(((@00000r rWcH|\}}}||}||}||}i} g} |D]I} |D]D} |D]?} d| || | z| z<#t$r| | | z| zY>sA%A* )A* c  tfdD}tfdD}tfdD}g}|D]1}|D],}|D]'}||z|z} | |vr| vr|| (-2dd} |D]@ d} fd dDD] } | vrd} | r|  A| S) aExtend a codon list to include all possible ambiguous codons. e.g.:: ['TAG', 'TAA'] -> ['TAG', 'TAA', 'TAR'] ['UAG', 'UGA'] -> ['UAG', 'UGA', 'URA'] Note that ['TAG', 'TGA'] -> ['TAG', 'TGA'], this does not add 'TRR' (which could also mean 'TAA' or 'TGG'). Thus only two more codons are added in the following: e.g.:: ['TGA', 'TAA', 'TAG'] -> ['TGA', 'TAA', 'TAG', 'TRA', 'TAR'] Returns a new (longer) list of codon strings. c3zK|]5\}}dDt|1|V6dS)ch|] }|d S)rr r!r;s r z2list_ambiguous_codons...! ) ) )E!H ) ) )r N issupersetsetr!lettermeaningscodonss r r+z(list_ambiguous_codons..c FH ) )& ) ) ) 4 4S]] C Cr c3zK|]5\}}dDt|1|V6dS)ch|] }|d S)rfr rts r ruz2list_ambiguous_codons...&rvr Nrwrzs r r+z(list_ambiguous_codons..#r~r c3zK|]5\}}dDt|1|V6dS)ch|] }|d S)r rts r ruz2list_ambiguous_codons...+rvr Nrwrzs r r+z(list_ambiguous_codons..(r~r NTcdg|],}dD]}dD] }||z|z -S)rfrr )r!r8r*r9 ambig_codonr^s r r#z)list_ambiguous_codons..:sq   1+a.A  1+a.A    GbL     r rF)rCitemsrg) r}r^c1_listc2_listc3_list candidatesr8r*r9r;r6wantedrs `` @r rZrZ s* ; A A C CG  ; A A C CG  ; A A C CG J-- - -B - -R"  **uF/B/B%%e,,, - - AAAYF!''      1+a.A    E F"" #  ' MM+ & & & Mr TGATAA)rrTRATAG)rrTARUAGUAA)rrUAR)rrr)rrrrrc,eZdZdZdZdZddZdZdS)rYz@Forward table for translation of ambiguous nucleotide sequences.c&||_||_||_i}|D]*\}}|D]"}||i}d||<|||<#+|D]\}}t |||<||_i|_dS)rrfN)rambiguous_nucleotideambiguous_proteinrgetrA _inverted_cache) rrrrinvertedrcvalcr"s r rzAmbiguousForwardTable.__init__xs*$8!!2*0022  ID#  LLB''$  ")) ' 'ID#!#YYHTNN! r cb ||dS#ttf$rYdSwxYw)zCheck if codon works as key for ambiguous forward_table. Only returns 'True' if forward_table[codon] returns a value. TF) __getitem__r5r)rr;s r __contains__z"AmbiguousForwardTable.__contains__sH     U # # #4*+   55 s ..NcR ||S#t$r|cYSwxYw)z,Implement get for dictionary-like behaviour.)rr5)rr;failobjs r rzAmbiguousForwardTable.gets? ##E** *   NNN s  &&c j|}|turt||turt||S#t$rYnwxYw j|}|j|<|S#t$rYnwxYw t |jj}nT#t$r tj|<t|dt$rtj|<t|wxYwt |dks Jdt |dkr|dj|<|dSi}|D].}j|D]}||ddz||</t |}g}| D] \}}||kr| |!t |dkrtj|<t|| fd|d}|j|<|S)aImplement dictionary-like behaviour for AmbiguousForwardTable. forward_table[codon] will either return an amino acid letter, or throws a KeyError (if codon does not encode an amino acid) or a TranslationError (if codon does encode for an amino acid, but either is also a stop codon or does encode several amino acids, for which no unique letter is available in the given alphabet. Nrzunambiguous codons must coderfc<tj||fSN)lenr)r"rs r z3AmbiguousForwardTable.__getitem__..sS)?)B%C%CQ$Gr )rF) rrr5rrprrrrrrgsort) rr;r"rkambiguous_possibler<termnrs ` r rz!AmbiguousForwardTable.__getitem__s  E"A$$$&u---H}}uoo%H    D  "5)A!"DK H    D  *-t)4+DHH , , ,!)DK 5//t + * * *!1DK "5)) ) *8}}q   "@    x==A  !)!DK A;   O OEu- O O+=+A+A$+J+JQ+N"4(( O MM,2244 ' 'JE3axx&&& x==A  !1DK "5)) )  GGGG HHH QK Es0 A AAA,, A98A9=BAC*r)rrr r rrrrr r r rYrYus`JJ&   MMMMMr rYcd|dddddD}t|||gz|||}t|tjtjtjtj}i} i} | D]*\} } | | | <| dd} | | | <| | | <+g} g}|D][} | | d| vr+| dd} | | | | \g}g}|D][} | | d| vr+| dd} | | | | \t|||gz| ||}ttj }d|d<t|d|tjtj}t|||gz| | |}t|tjtj tjtj}|dkr|a|a|t$|<|t&|<|t(|<|t*|<|t,|<|t.|<|| ||D]>}|t0|<|t2|<|t4|<|t6|<|t8|<|t:|<?dS) z_Turn codon table data into objects (PRIVATE). The data is stored in the dictionaries. c6g|]}|Sr )stripr s r r#z'register_ncbi_table..s-       r z and z; rr$UNrf)replacesplitrPrWrambiguous_dna_lettersambiguous_dna_valuesextended_protein_lettersextended_protein_valuesrrgrIr>ambiguous_rna_valuesrTambiguous_rna_lettersstandard_dna_tablestandard_rna_tableunambiguous_dna_by_idunambiguous_rna_by_id generic_by_idambiguous_dna_by_idambiguous_rna_by_idambiguous_generic_by_idunambiguous_dna_by_nameunambiguous_rna_by_namegeneric_by_nameambiguous_dna_by_nameambiguous_rna_by_nameambiguous_generic_by_name)rcalt_namer2rDrrr3dna ambig_dna rna_table generic_tabler;rrna_start_codonsgeneric_start_codonsrna_stop_codonsgeneric_stop_codonsgeneric_merged_values ambig_genericrna ambig_rnas r register_ncbi_tablersi  <<66>>tTJJPPQUVV   E B 2E< U UC# '&*) IIMkkmm s" e c3''" e %''##E*** %<<MM#s++E ' ' . . .&&&&O&&""5))) %<<MM#s++E  & &u - - -u%%%% EXJ  /CEXG )8>>@@AANN3' *) M  EXJ  +;_  C$ '&*) I Qww   #" #"M"''"/B X88(+%(+% '&/d#&/d#*7!$'' 88r StandardSGC0rfTTTFTTCTTALTTGTCTSTCCTCATCGTATYTACTGTCTGCTGGWCTTCTCCTACTGCCTPCCCCCACCGCATHCACCAAQCAGCGTRCGCCGACGGATTIATCATAATGMACTr$ACCACAACGAATNAACAAAKAAGAGTAGCAGAAGGGTTVGTCGTAGTGGCTAGCCDEG) GCAGCGGATGACGAAGAGGGTGGCGGAGGG)rrr)rrr)rcrr2rDrrzVertebrate MitochondrialSGC1rr) rrr r!r"r#r$r%r&)rrrr)rrrrrzYeast MitochondrialSGC2) rrrrr r!r"r#r$r%r&)rrrz`Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; SpiroplasmaSGC3)rrrrrrrrzInvertebrate MitochondrialSGC4)rrrrrrz8Ciliate Nuclear; Dasycladacean Nuclear; Hexamita NuclearSGC5) rrrrrr r!r"r#r$r%r&z0Echinoderm Mitochondrial; Flatworm MitochondrialSGC8 zEuplotid NuclearSGC9 z%Bacterial, Archaeal and Plant Plastid )rrrrrrrzAlternative Yeast Nuclear zAscidian Mitochondrial )rrrrz"Alternative Flatworm MitochondrialzBlepharisma MacronuclearzChlorophycean MitochondrialzTrematode Mitochondrialz"Scenedesmus obliquus Mitochondrial)rrrzThraustochytrium Mitochondrial)rrrr)rrrzPterobranchia Mitochondrial)rrrrz*Candidate Division SR1 and Gracilibacteria)rrrzPachysolen tannophilus NuclearzKaryorelict Nuclear) rrrrrrr r!r"r#r$r%r&zCondylostoma NuclearzMesodinium NuclearzPeritrich NuclearzBlastocrithidia NuclearzBalanophoraceae Plastid zCephalodiscidae Mitochondrial!)!r typingrBio.Datarrrrrrrrrrrrrrr ExceptionrrrGrIrPrTrWrprZrrrYrr r r rJsN 99999y999bbbbbbbbJ   WWWWWZWWW(<<<<<<<< <<<<<<<<%0%0%0%0%0*%0%0%0P4>>>BeU^Y-KLLQQQ eU^Y-KLL  QeU^Y-KLLQQQ eU^Y-KLLQQQ 222I4RSSXXX0uuuuuuuup`8`8`8\    s 3  %s ,13  s 3  %s ,13  s 3  s  3  -23   s   3   !&s   -23    s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s   3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3  (+33s33s3!   $&%%&&&/4 #   s 3  %s ,13  s 3  %s ,13  s 3  s  3  !&s  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3  s 3 !&s -23  s 3 !&s  473s33s3!   $-,,444/4    s 3  %s ,13  s 3  %s ,13  s 3  s  3  !&s  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $&&&/4 -   s 3  %s ,13  s 3  %s ,13  s 3  s  3  !&s  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $III16 %   s 3  %s ,13  s 3  %s ,13  s 3  s  3  !&s  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $;;;/4 C   s 3  %s ,13  s 3  %s ,13  s 3 !&s -23  s  3  -23   s   3    !&s   -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s   -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  3s33s33s3!   $/4 ;   s 3  %s ,13  s 3  %s ,13  s 3  s  3  !&s  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $/4     s 3  %s ,13  s 3  %s ,13  s 3  s  3  !&s  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $/4 0    s 3  %s ,13  s 3  %s ,13  s 3  s  3  -23   s   3   !&s   -23    s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s   3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3  (+33s33s3!   $&%%BBB/4 $    s 3  %s ,13  s 3  %s ,13  s 3  s  3  -23   s   3   !&s   -23    s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s   3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3  (+33s33s3!   $&%%/4 !    s 3  %s ,13  s 3  %s ,13  s 3  s  3  !&s  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $---/4 -    s 3  %s ,13  s 3  %s ,13  s 3 !&s  s  3  !&s  -23   s   3    !&s   -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s   -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  3s33s33s3!   $/4 #    s 3  %s ,13  s 3  %s ,13  s 3 -23  s  3  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $/4 &    s 3  %s ,13  s 3  %s ,13  s 3 -23  s  3  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $/4 "    s 3  %s ,13  s 3  %s ,13  s 3  s  3  !&s  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $/4 -    s 3  %s ,13  s 3 ,13  s 3 -23  s  3  -23   s   3   !&s   -23    s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s   3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3  (+33s33s3!   $&%%/4 )    s 3 ,13  s 3  %s ,13  s 3  s  3  -23   s   3   !&s   -23   s    3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3   !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s  473s33s3!   $-,,&&&/4 &    s 3  %s ,13  s 3  %s ,13  s 3  s  3  !&s  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $---/4 5    s 3  %s ,13  s 3  %s ,13  s 3  s  3  !&s  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $&&&/4 )    s 3  %s ,13  s 3  %s ,13  s 3  s  3  -23   s   3   !&s   -23    s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s   3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3  (+33s33s3!   $&%%/4     s 3  %s ,13  s 3  %s ,13  s 3 !&s -23  s  3  !&s  -23   s    3   !&s   -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3   !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s  473s33s33s3!   $/4     s 3  %s ,13  s 3  %s ,13  s 3 !&s -23  s  3  !&s  -23   s    3   !&s   -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3   !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s  473s33s33s3!   $&%%/4     s 3  %s ,13  s 3  %s ,13  s 3 !&s -23  s  3  -23   s   3    !&s   -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s   -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  3s33s33s3!   $/4     s 3  %s ,13  s 3  %s ,13  s 3 !&s -23  s  3  -23   s   3    !&s   -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s   -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  3s33s33s3!   $/4 "    s 3  %s ,13  s 3  %s ,13  s 3 !&s -23  s  3  !&s  -23   s    3   !&s   -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3   !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s  473s33s33s3!   $/4 "    s 3  %s ,13  s 3  %s ,13  s 3 -23  s  3  -23   s   3   !&s    -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s -23    s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s  s33s33s3!   $BBB/4 (    s 3  %s ,13  s 3  %s ,13  s 3 !&s  s  3  !&s  -23   s   3    !&s   -23   s   3   !&s   -23   s 3 !&s -23  s 3 !&s -23  s 3 !&s   -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  s 3 !&s -23  3s33s33s3!   $---/r