RiM)dZddlmZddlmZiZiZiZiZiZ iZ iZ iZ iZ iZiZiZdadaGddeZGddZd ZGd d eZGd d eZGddeZGddeZdZdZeddgej:gdk(sJeddgej:ddgk(sJeddgej:gdk(sJeddgej<gdk(sJegdej:gdk(sJGddZd 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 dggdny)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) IUPACDataNceZdZdZy)TranslationErrorz.Container for translation specific exceptions.N)__name__ __module__ __qualname____doc__K/home/agent/.friday_env/lib/python3.12/site-packages/Bio/Data/CodonTable.pyrr,s8r rceZdZUdZiZeeefed<iZeeefed<gZ e eed<gZ e eed<ddeee e fdedzdedzdeeefdeeefde ede ed dfd Z d Z y) CodonTablezA codon-table, or genetic code. forward_table back_table start_codons stop_codonsNnucleotide_alphabetprotein_alphabetreturncX||_||_||_||_||_||_yInitialize the class.N)rrrrrr)selfrrrrrrs r __init__zCodonTable.__init__9s3$7 0*$(&r c|jrd|jz}nd}|jr2|ddj|jDcgc]}|s| c}zz }|j}|d|vrd}nd}|dz }|d d jd |Dzd zz }|d d jd|Dzdzz }|D]}|D]s}|dz}|D]W}||z|z}|d|z }||jvr|dz }' |j |} ||jvr |d| dz }O|d| dz }Y|d|zz }|d|zz }u|d d jd|Dzdzz }|Scc}w#t $rd} Ylt$rd} YxwxYw)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 , TTCAGUCAGz z ||c3(K|] }d|d yw)z z Nr .0c2s r z%CodonTable.__str__..zs"ErRt6?"Esz --++c3 K|]}dywz ---------Nr r$s r r'z%CodonTable.__str__..{s$CR[$C z+--z |z Stop|?z(s)|z | c3 K|]}dywr*r r$s r r'z%CodonTable.__str__..s(G(Gr+) idnamesjoinrrrKeyErrorrr) ranswerxlettersc1c3liner&codonaminos r __str__zCodonTable.__str__Js: 77$'')F'F :: cDII$**&BQq&BCC CF**  3'>GG &%#(("EW"EEEKK'CHH$C7$CCCeKK PB &Dy!4BGbLEawK'D 0 00(($($6$6u$=E !D$5$55 awdO3D awdO3D4 b $+%' &( g(Gw(G GG%O OF+ P, M'C6 (($'E/($'E(s$E E 4E"" E< / E< ;E< )rrr r rdictstr__annotations__rrlistrrr;r r r rr0s)$&M4S>&!#JS#X# L$s) Kc +/'+(5%/".!,' 4Z'*'CH~ ' cN ' 3i '#Y' '"Hr rcDi}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_tablerEs:Je}%!$ 5:%)Jt r cJeZdZUdZdZedzed<ejZ dZ dZ y)NCBICodonTablez-Codon table for generic nucleotide sequences.Nrcr||_||_||_t||d|_||_||_y)rrN)r/r0rrErrr)rr/r0rBrrs r rzNCBICodonTable.__init__s: ")%Q@(&r ch|jjd|jd|jdS)z?Represent the NCBI codon table class as a string for debugging.z(id=z, names=z, ...)) __class__rr/r0)rs r __repr__zNCBICodonTable.__repr__s...))*$twwk$**vVVr ) rrr r rr=r>rprotein_lettersrrrKr r r rGrGs+7&*t* 00'Wr rGc(eZdZdZej Zy)NCBICodonTableDNAz*Codon table for unambiguous DNA sequences.N)rrr r runambiguous_dna_lettersrr r r rNrN4#;;r rNc(eZdZdZej Zy)NCBICodonTableRNAz*Codon table for unambiguous RNA sequences.N)rrr r runambiguous_rna_lettersrr r r rRrRrPr rRceZdZdZdZdZy)AmbiguousCodonTablez)Base codon table for ambiguous sequences.c tj|||t|j|||jt |j |t |j|||_yr) rrAmbiguousForwardTablerrlist_ambiguous_codonsrr _codon_table)r codon_tableambiguous_nucleotide_alphabetambiguous_nucleotide_valuesambiguous_protein_alphabetambiguous_protein_valuess r rzAmbiguousCodonTable.__init__sp   ) & !))+(   " " "((*E  "+"9"9;V W! $(r c.t|j|S)z0Forward attribute lookups to the original table.)getattrrY)rnames r __getattr__zAmbiguousCodonTable.__getattr__st(($//r N)rrr r rrbr r r rUrUs3(@0r rUc|\}}}||}||}||}i} g} |D]} |D]} |D]} d| || | z| z<!| r| rtd|dt|t| S#t$r| j| | z| zYcwxYw)z /LLb2./sA'' B B c &tfd|jD}tfd|jD}tfd|jD}g}|D]3}|D],}|D]%}||z|z} | |vs| vs|j| '.5dd} |D]^} d} || dDcgc]$}|| dD]}|| dD] }||z|z &c}}}D] } | vsd } | sN| j| `| Scc}}}w) 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. c3K|]4\}}Dchc]}|d c}jt|r|6ycc}ww)rN issupersetsetr%lettermeaningsr9codonss r r'z(list_ambiguous_codons..C FH"( )E!H ) 4 4S] C  * A ='Ac3K|]4\}}Dchc]}|d c}jt|r|6ycc}ww)rdNrqrts r r'z(list_ambiguous_codons..#rxryc3K|]4\}}Dchc]}|d c}jt|r|6ycc}ww)Nrqrts r r'z(list_ambiguous_codons..(rxryNTrrdr|F)rAitemsre) rwr\c1_listc2_listc3_list candidatesr6r&r7r9r3 ambig_codonwanteds ` r rXrX s* ; A A CG  ; A A CG  ; A A CG J- -B -R"  *uF/B%%e, - -- AYF!' 2+a.A  1+a.A 1+a.A   GbL   E F"   MM+ &' M s:)D TGATAA)rrTRATAG)rrTARUAGUAA)rrUAR)rrr)rrrrrc*eZdZdZdZdZddZdZy)rWz@Forward table for translation of ambiguous nucleotide sequences.c||_||_||_i}|jD](\}}|D]}|j |i}d||<|||< *|jD]\}}t |||<||_i|_y)rrdN)rambiguous_nucleotideambiguous_proteinr}getr? _inverted_cache) rrrrinvertedravalcr4s r rzAmbiguousForwardTable.__init__xs*$8!!2*002 ID# LLB'$   ") 'ID#!#YHTN '! r cR |j|y#ttf$rYywxYw)zCheck if codon works as key for ambiguous forward_table. Only returns 'True' if forward_table[codon] returns a value. TF) __getitem__r2r)rr9s r __contains__z"AmbiguousForwardTable.__contains__s0     U #*+  s &&NcH |j|S#t$r|cYSwxYw)z,Implement get for dictionary-like behaviour.)rr2)rr9failobjs r rzAmbiguousForwardTable.gets, ##E* * N s  !!c j|}|tur t||tur t||S#t$rYnwxYw j|}|j|<|S#t$rYnwxYw t |jj }nR#t$r tj|<t|dt$rtj|<t|wxYwt |dkDsJdt |dk(r|dj|<|dSi}|D].}j|D]}|j|ddz||<0t |}g}|jD]\}}||k(s |j|t |dk(rtj|<t||jfd|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 coderdc8tj||fSN)lenr)r4rs r z3AmbiguousForwardTable.__getitem__..sS)?)?)B%CQ$Gr )rD) rrr2rrnrrrrr}resort) rr9r4riambiguous_possibler:termnrs ` r rz!AmbiguousForwardTable.__getitem__s%  E"A$$&u--H}uo%H    ""5)A!"DKK H    *-t))4+D+DH ,!)DKK 5/t + *!1DKK "5) ) *8}q @"@@  x=A !)!DKK A;   OEu- O+=+A+A$+JQ+N"4( O O M,224 'JE3ax& ' x=A !1DKK "5) )  G H QK Es.: AA A** A65A6:!BAC+r)rrr r rrrrr r r rWrWusJ& Mr rWc|jddjddjdDcgc]}|j}}t|||gz|||}t |t j t jt jt j} i} i} |jD]&\} } | | | <| jdd} | | | <| | | <(g}g}|D]K} |j| d| vr#| jdd} |j| |j| Mg}g}|D]K} |j| d| vr#| jdd} |j| |j| Mt|||gz| ||}tt jj}d|d<t |d|t jt j}t|||gz| ||}t |t j t jt jt j}|dk(r|a|a|t&|<|t(|<|t*|<| t,|<|t.|<|t0|<||j||D]8}|t2|<|t4|<|t6|<| t8|<|t:|<|t<|<:ycc}w)z_Turn codon table data into objects (PRIVATE). The data is stored in the dictionaries. z and z; rrUNrd)replacesplitstriprNrUrambiguous_dna_lettersambiguous_dna_valuesextended_protein_lettersextended_protein_valuesr}rerGr<ambiguous_rna_valuesrRambiguous_rna_lettersstandard_dna_tablestandard_rna_tableunambiguous_dna_by_idunambiguous_rna_by_id generic_by_idambiguous_dna_by_idambiguous_rna_by_idambiguous_generic_by_idunambiguous_dna_by_nameunambiguous_rna_by_namegeneric_by_nameambiguous_dna_by_nameambiguous_rna_by_nameambiguous_generic_by_name)raalt_namer/rBrrr4r0dna ambig_dna rna_table generic_tabler9rrna_start_codonsgeneric_start_codonsrna_stop_codonsgeneric_stop_codonsgeneric_merged_values ambig_genericrna ambig_rnas r register_ncbi_tablers <<6>>tTJPPQUV   E  B 2E< UC# ''&&**)) IIMkkm s" e c3'" e %  '##E* %<MM#s+E ' ' .&'O&""5) %<MM#s+E  & &u -u% & EXJ  /CEXG )88>>@ANN3' **)) M  EXJ  +;_ C$ ''&&**)) I Qw   #" #"M"''"/B X8(+%(+% '&/d#&/d#*7!$' 8e sK StandardSGC0rdTTTFTTCTTALTTGTCTSTCCTCATCGTATYTACTGTCTGCTGGWCTTCTCCTACTGCCTPCCCCCACCGCATHCACCAAQCAGCGTRCGCCGACGGATTIATCATAATGMACTrACCACAACGAATNAACAAAKAAGAGTAGCAGAAGGGTTVGTCGTAGTGGCTAGCCDEG) GCAGCGGATGACGAAGAGGGTGGCGGAGGG)rrr)rrr)rarr/rBrrzVertebrate MitochondrialSGC1r|r) rrrrrrrrr)rrrr)rrrrr zYeast MitochondrialSGC2) rrrrrrrrrrr)rrr z`Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; SpiroplasmaSGC3)rrrrrrrr zInvertebrate MitochondrialSGC4)rrrrrr z8Ciliate Nuclear; Dasycladacean Nuclear; Hexamita NuclearSGC5) rrrrrrrrrrrrz0Echinoderm Mitochondrial; Flatworm MitochondrialSGC8 zEuplotid NuclearSGC9 z%Bacterial, Archaeal and Plant Plastid )rrrrrrr zAlternative Yeast Nuclear zAscidian Mitochondrial )rrrr z"Alternative Flatworm MitochondrialzBlepharisma MacronuclearzChlorophycean MitochondrialzTrematode Mitochondrialz"Scenedesmus obliquus Mitochondrial)rrrzThraustochytrium Mitochondrial)rrrr)rrr zPterobranchia Mitochondrial)rrrr z*Candidate Division SR1 and Gracilibacteria)rrr zPachysolen tannophilus NuclearzKaryorelict Nuclear) r rrrrrrrrrrrrzCondylostoma NuclearzMesodinium NuclearzPeritrich NuclearzBlastocrithidia NuclearzBalanophoraceae Plastid zCephalodiscidae Mitochondrial!)!r typingrBio.Datarrrrrrrrrrrrrrr ExceptionrrrErGrNrRrUrnrXrrrWrr r r rAsG 9y9bbJ WZW(<< <<%0*%0P4>BeU^Y-K-KLQ eU^Y-K-KL  QeU^Y-K-KLQ eU^Y-K-KLQ 2I4R4RSX0uup`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! $-4/4    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! $I16 %   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! $&B/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! 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