o RŀgV@sX(dZddlmZddlmZiZiZiZiZiZ iZ iZ iZ iZ iZiZiZdadaGdddeZGdddZd d ZGd d d eZGd ddeZGdddeZGdddeZddZddZeddgejgdkssJeddgejddgksJeddgejgdksJeddgejgdksJegdejgd ksJGd!d"d"Zd#d$Z e d%d&d'id(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7d9d:d;d,dd,id?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTdUdVidWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdkdjdjdjdldldmdmdndndndndo gdpgdqdre dsdtduid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7dd:d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdTdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dddedfdedgdedhdedidjdkdjdvdjdjdldldmdmdndndndndw gdxgdydre dzd{d|id(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7dd:d9d:d;dVddVd?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdTdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddggd~dre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7dd:d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddggddre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7dd:d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdTdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbd/dcd/dddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddggddre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4ddHddHd6d7d8d7d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPidSdTdUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedjdjdjdjdldldmdmdndndndnd dgdSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7dd:d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d[d_d^d`d/dad/dbd/dcd/dddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddgdSdhgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7dd7d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddgdSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7d9d:d;d,dd,id?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTdUdVidWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdkdjdjdjdldldmdmdndndndndo gdpgddre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7d9d:d;d,dd/id?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTdUdVidWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdkdjdjdjdldldmdmdndndndndo gdpd>dSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7dd:d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdTdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdndcdndddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddggddre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4dd4d6d7d8d7dd:d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPidSdTdUdVdWdVdXdVdYdVdZd[d\d[d]d[d_d^d`d/dad/dbd/dcd/dddedfdedgdedhdedjdjdjdjdldldmdmdndndndnd dgdSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4ddHd6d7d8d7d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddgdSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4dd,d6d7d8d7d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddgdSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7dd:d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdTdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d[d_d^d`d/dad/dbd/dcd/dddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddgdSdhgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d2d/d3d4d5d4dd,d6d7d8d7d9d:d;d,dd,id?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTdUdVidWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdkdjdjdjdldldmdmdndndndndo gddSgdre dddid(d)d*d)d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7d9d:d;d,dd,d?d@idAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTdUdVdWdVidXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdkdjdvdjdjdldldmdmdndndndndw gdgddre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7dd:d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbd/dcd^dddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddggddre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7ddnd9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddggddre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4d6d7d8d7d9d:d;d,ddjid?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTdUdVidWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdkdjdjdjdldldmdmdndndndndo gdpd>dSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4ddHddHd6d7d8d7dd:d9d:d;d,idd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPidRdPdSdTdUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdededjdjdjdjdldldmdmdndndndnd dgdSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4ddHddHd6d7d8d7dd:d9d:d;d,idd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPidRdPdSdTdUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdededjdjdjdjdldldmdmdndndndnd gdpdSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4dd4dd4d6d7d8d7d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPidSdTdUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedjdjdjdjdldldmdmdndndndnd dgdSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4ddmddmd6d7d8d7d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPidSdTdUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedjdjdjdjdldldmdmdndndndnd dgdSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4ddmddmd6d7d8d7dd:d9d:d;d,idd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPidRdPdSdTdUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdededjdjdjdjdldldmdmdndndndnd ddgdSgdre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4dd:d6d7d8d7d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPdSdTidUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbdKdcdKdddedfdedgdedhdedidjdjdjdjdldldmdmdndndndnd} ddggddre dddid(d)d*d)d+d,d-d,d.d/d0d/d1d/d2d/d3d4d5d4dd4d6d7d8d7dd:d9d:d;d,dd,d?d@dAd@dBd@dCd@dDdEdFdEdGdHdIdHdJdKdLdKdMdKdNdKdOdPdQdPdRdPidSdTdUdVdWdVdXdVdYdVdZd[d\d[d]d^d_d^d`d/dad/dbd/dcd^dddedfdedgdedhdedjdjdjdjdldldmdmdndndndnd dggddrdS)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) IUPACDataNc@seZdZdZdS)TranslationErrorz.Container for translation specific exceptions.N)__name__ __module__ __qualname____doc__r r G/var/www/html/myenv/lib/python3.10/site-packages/Bio/Data/CodonTable.pyr,src@seZdZUdZiZeeefed<iZeeefed<gZ e eed<gZ e eed<ddeee e fde ede edeeefdeeefde ede ed dfd d Z d d ZdS) CodonTablezA codon-table, or genetic code. forward_table back_table start_codons stop_codonsNnucleotide_alphabetprotein_alphabetreturncCs(||_||_||_||_||_||_dSInitialize the class.N)rrr r rr)selfrrr r rrr r r __init__9s   zCodonTable.__init__c Cs|jr d|j}nd}|jr|dddd|jD7}|j}|dur+d|vr+d }nd }|d 7}|d d dd|Dd 7}|dddd|Dd7}|D]v}|D]a}|d}|D]L}|||}|d|7}||jvrx|d7}q_z|j|}Wntyd}Yn tyd}Ynw||jvr|d|d7}q_|d|d7}q_|d|7}|d|7}qW|dddd|Dd7}qS|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 , cSsg|]}|r|qSr r .0xr r r lz&CodonTable.__str__..NTTCAGUCAGz z ||css|] }d|dVqdS)z z Nr rc2r r r zsz%CodonTable.__str__..z --++cs|]}dVqdSz ---------Nr r"r r r r${z+--z |z Stop|?z(s)|z | csr&r'r r"r r r r$r() idnamesjoinrrr KeyErrorrr) ranswerlettersc1c3liner#codonaminor r r __str__JsD          "zCodonTable.__str__)rrrrr dictstr__annotations__r rlistrrrr6r r r r r 0s8    r cCs*i}t|D]}||||<q||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_codonr keyr r r make_back_tables  r?c@s8eZdZUdZdZeeed<ej Z ddZ ddZ dS)NCBICodonTablez-Codon table for generic nucleotide sequences.NrcCs2||_||_||_t||d|_||_||_dS)rrN)r+r,r r?r rr)rr+r,r<rrr r r rs  zNCBICodonTable.__init__cCs|jjd|jd|jdS)z?Represent the NCBI codon table class as a string for debugging.z(id=z, names=z, ...)) __class__rr+r,rr r r __repr__szNCBICodonTable.__repr__) rrrrrrr8r9rprotein_lettersrrrCr r r r r@s  r@c@eZdZdZejZdS)NCBICodonTableDNAz*Codon table for unambiguous DNA sequences.N)rrrrrunambiguous_dna_lettersrr r r r rF rFc@rE)NCBICodonTableRNAz*Codon table for unambiguous RNA sequences.N)rrrrrunambiguous_rna_lettersrr r r r rIrHrIc@s eZdZdZddZddZdS)AmbiguousCodonTablez)Base codon table for ambiguous sequences.c Cs<t|||t|j|||jt|j|t|j|||_dSr) r rAmbiguousForwardTabler r list_ambiguous_codonsrr _codon_table)r codon_tableambiguous_nucleotide_alphabetambiguous_nucleotide_valuesambiguous_protein_alphabetambiguous_protein_valuesr r r rs    zAmbiguousCodonTable.__init__cCs t|j|S)z0Forward attribute lookups to the original table.)getattrrN)rnamer r r __getattr__s zAmbiguousCodonTable.__getattr__N)rrrrrrVr r r r rKs rKc Cs|\}}}||}||}||}i} g} |D]*} |D]%} |D] } z d| || | | <Wqty?| | | | Yqwqq| rR| rNtd|dt|t| S)z ['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. c30|]\}}ddDt|r|VqdS)cSh|]}|dqS)rr rr4r r r !r2list_ambiguous_codons...N issupersetsetrlettermeaningscodonsr r r$ z(list_ambiguous_codons..c3rb)cSrc)rWr rdr r r re&rrfNrgrjrmr r r$#roc3rb)cSrc)r rdr r r re+rrfNrgrjrmr r r$(roNTcs<g|]}dD]}dD]}|||qq qS)rWrpr )rr1r#r2) ambig_codonrQr r r:s   z)list_ambiguous_codons..rF)r;itemsrX) rnrQc1_listc2_listc3_list candidatesr1r#r2r4r/wantedr )rqrQrnr rM sB          rMTGATAA)rxryTRATAG)r{ryTARUAGUAA)r}r~UAR)rxryr{)rxryr{r|rzc@s2eZdZdZddZddZd ddZd d ZdS) rLz@Forward table for translation of ambiguous nucleotide sequences.c Cs|||_||_||_i}|D]\}}|D]}||i}d||<|||<qq|D] \}}t|||<q+||_i|_dS)rrWN)r ambiguous_nucleotideambiguous_proteinrrgetr: _inverted_cache) rr rrinvertedrUvalcrr r r rxs   zAmbiguousForwardTable.__init__c Cs*z||WdSttfyYdSw)zCheck if codon works as key for ambiguous forward_table. Only returns 'True' if forward_table[codon] returns a value. TF) __getitem__r.r)rr4r r r __contains__s  z"AmbiguousForwardTable.__contains__NcCs$z||WSty|YSw)z,Implement get for dictionary-like behaviour.)rr.)rr4failobjr r r rs   zAmbiguousForwardTable.getc szj|}Wn tyYnw|turt||tur!t||Sz j|}|j|<|WSty9Ynwz t|jj}Wn tyUtj|<t|dtydtj|<t|wt|dksoJdt|dkr|dj|<|dSi}|D]}j|D] }||dd||<qqt|}g}| D] \}}||kr| |qt|dkrtj|<t||j fddd|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 coderWcstj||fSN)lenr)rrBr r sz3AmbiguousForwardTable.__getitem__..)r>) rr.rr rarrrrrrrXsort) rr4rr\ambiguous_possibler5termnrr rBr rsd                 z!AmbiguousForwardTable.__getitem__r)rrrrrrrrr r r r rLus  rLcCsdd|dddddD}t|||g|||}t|tjtjtjtj}i} i} | D]\} } | | | <| dd} | | | <| | | <q1g} g}|D]} | | d| vrd| dd} | | | | qNg}g}|D]} | | d| vr| dd} | | | | qpt |||g| ||}t tj }d|d<t|d|tjtj}t|||g| | |}t|tjtj tjtj}|d kr|a|a|t|<|t|<|t|<|t|<|t|<|t|<|dur| ||D]}|t|<|t|<|t|<|t|<|t|<|t|<qdS) z_Turn codon table data into objects (PRIVATE). 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