3 :>"^E@spdZddlmZddlmZddlmZiZiZiZ iZ iZ iZ iZ iZiZiZiZiZdadaGdddeZGdd d eZd d ZGd d d eZGdddeZGdddeZGdddeZddZddZeddgej dddgkst!eddgej ddgkst!eddgej dddgks4t!eddgej"dddgksTt!edddgej dddddgkszt!Gd d!d!eZ#d"d#Z$e$d$d%d&d'd'd(d(d)d)d)d)d*d*d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:d;=dddgdgd?e$d@dAdBd'd'd(d(d)d)d)d)d*d*d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d2d2d3d3d3d3d4d4d5d5d)d)d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dCdIgd?e$dJdKdLd'd'd(d(d)d)d)d)d*d*d+d+d,d,d3d3d3d3d-d-d-d-d.d.d/d/d0d0d0d0d1d1d2d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dM>ddgdHd>dIgd?e$dNdOdPd'd'd(d(d)d)d)d)d*d*d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dM>ddgdQddIgd?e$dRdSdTd'd'd(d(d)d)d)d)d*d*d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d2d2d3d3d3d3d4d4d5d5d)d)d)d)d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dM>ddgddIgd?e$dUdVdWd'd'd(d(d)d)d)d)d*d*d/d/d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dX?dgd>gd?e$dYdZd[d'd'd(d(d)d)d)d)d*d*d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d4d5d)d)d)d)d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dM>ddgd>dIgd?e$d\d]d^d'd'd(d(d)d)d)d)d*d*d+d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dM>ddgd>gd?e$d_dd`d'd'd(d(d)d)d)d)d*d*d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:d;=dddgddIgd?e$daddbd'd'd(d(d)d)d)d)d*d*d+d+d,d(d(d(d)d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:d;=dddgd=d>gd?e$dcdddd'd'd(d(d)d)d)d)d*d*d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d2d2d3d3d3d3d4d4d5d5d)d)d:d:d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dM>ddgddIgd?e$deddfd'd'd(d(d)d)d)d)d*d*d*d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d4d5d)d)d)d)d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dg?dgd>gd?e$dhddid'd'd(d(d)d)d)d)d*d*d/d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dj>ddgd>gd?e$dkddld'd'd(d(d)d)d)d)d*d*d(d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dj>ddgd>gd?e$dmddnd'd'd(d(d)d)d)d)d*d*d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d2d2d3d3d3d3d4d4d4d5d)d)d)d)d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dM>ddgd>dIgd?e$doddpd'd'd(d(d)d)d)d*d*d(d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dq=drddgd>gd?e$dsddtd'd'd(d)d)d)d)d*d*d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dudIgd?e$dvddwd'd'd(d(d)d)d)d)d*d*d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d)d5d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dM>ddgddIgd?e$dxddyd'd'd(d(d)d)d)d)d*d*d+d+d:d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dM>ddgddIgd?e$dzdd{d'd'd(d(d)d)d)d)d*d*d+d+d,d(d(d(d7d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:d;=dddgd=d>gd?e$d|dd}d'd'd(d(d)d)d)d)d*d*d/d/d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:d~@dgd>gd?e$dddd'd'd(d(d)d)d)d)d*d*d/d/d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:d~@dddgd>gd?e$dddd'd'd(d(d)d)d)d)d*d*d*d*d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dX?dgd>gd?e$dddd'd'd(d(d)d)d)d)d*d*d9d9d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:dX?dgd>gd?e$dddd'd'd(d(d)d)d)d)d*d*d9d9d+d+d,d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:d~@ddgd>gd?e$dddd'd'd(d(d)d)d)d)d*d*d,d+d+d,d(d(d(d(d-d-d-d-d.d.d/d/d0d0d0d0d1d1d1d2d3d3d3d3d4d4d5d5d)d)d0d0d6d6d6d6d7d7d7d7d8d8d9d9d:d:d:d:d>dddgddIgd?dS)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) )Alphabet)IUPAC) IUPACDataNc@seZdZdZdS)TranslationErrorz.Container for translation specific exceptions.N)__name__ __module__ __qualname____doc__r r c/home/psgendb/BIRCHDEV/lib-linux-x86_64/python/lib64/python3.5/site-packages/Bio/Data/CodonTable.pyr-src@sJeZdZdZejZejZiZ iZ gZ gZ eee e e e fddZ ddZdS) CodonTablezA codon-table, or genetic code.cCs(||_||_||_||_||_||_dS)zInitialize the class.N)nucleotide_alphabetprotein_alphabet forward_table back_table start_codons stop_codons)selfr rrrrrr r r __init__?s zCodonTable.__init__c Cs|jrd|j}nd}|jr:|ddjdd|jD7}|jj}t|jtjs`|dk rfd|krfd }nd }|d 7}|d d jdd|Dd 7}|ddjdd|Dd7}x|D]}x|D]}|d}x|D]}|||}|d|7}||jkr|d7}qy|j |}Wn2t k r.d}Ynt k rFd}YnX||j krb|d|7}q|d|7}qW|d|7}|d|7}qW|ddjdd|Dd7}qW|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 z, cSsg|] }|r|qSr r ).0xr r r msz&CodonTable.__str__..NTZTCAGZUCAGz z ||css|]}d|VqdS)z %s Nr )rc2r r r |sz%CodonTable.__str__..z --++css|] }dVqdS)z ---------Nr )rrr r r r}sz+--z |z %sz Stop|?z %s(s)|z %s | css|] }dVqdS)z ---------Nr )rrr r r rs) idnamesjoinr letters isinstancer DNAAlphabetrrKeyErrorrr) ranswerr#c1c3linercodonaminor r r __str__KsD             $zCodonTable.__str__N)rrrr rgeneric_nucleotider generic_proteinrrrrrrr-r r r r r 3s r cCs.i}xt|D]}||||<qW||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)tableZdefault_stop_codonrkeyr r r make_back_tables r3c@s,eZdZdZejZejZ ddZ ddZ dS)NCBICodonTablez-Codon table for generic nucleotide sequences.cCs2||_||_||_t||d|_||_||_dS)zInitialize the class.rN)r r!rr3rrr)rr r!r1rrr r r rs zNCBICodonTable.__init__cCsd|jj|j|jfS)z?Represent the NCBI codon table class as a string for debugging.z%s(id=%r, names=%r, ...)) __class__rr r!)rr r r __repr__szNCBICodonTable.__repr__N) rrrr rr.r rproteinrrr6r r r r r4s  r4c@seZdZdZejZdS)NCBICodonTableDNAz*Codon table for unambiguous DNA sequences.N)rrrr runambiguous_dnar r r r r r8sr8c@seZdZdZejZdS)NCBICodonTableRNAz*Codon table for unambiguous RNA sequences.N)rrrr runambiguous_rnar r r r r r:sr:c@s eZdZdZddZddZdS)AmbiguousCodonTablez)Base codon table for ambiguous sequences.c Cs<tj|||t|j|||jt|j|t|j|||_dS)zInitialize the class.N) r rAmbiguousForwardTablerrlist_ambiguous_codonsrr _codon_table)r codon_tableZambiguous_nucleotide_alphabetambiguous_nucleotide_valuesZambiguous_protein_alphabetZambiguous_protein_valuesr r r rszAmbiguousCodonTable.__init__cCs t|j|S)z0Forward attribute lookups to the original table.)getattrr?)rnamer r r __getattr__szAmbiguousCodonTable.__getattr__N)rrrr rrDr r r r r<sr<cCs|\}}}||}||}||}i} g} xh|D]`} xZ|D]R} xL|D]D} yd| || | | <WqDtk r| j| | | YqDXqDWq:Wq0W| r| rtd|t|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. c3s.|]&\}}ddDjt|r|VqdS)cSsh|] }|dqS)rr )rr+r r r sz2list_ambiguous_codons...N) issupersetset)rlettermeanings)codonsr r rsz(list_ambiguous_codons..c3s.|]&\}}ddDjt|r|VqdS)cSsh|] }|dqS)rEr )rr+r r r rM sz2list_ambiguous_codons...N)rNrO)rrPrQ)rRr r rsc3s.|]&\}}ddDjt|r|VqdS)cSsh|] }|dqS)r )rr+r r r rM$sz2list_ambiguous_codons...N)rNrO)rrPrQ)rRr r r"sNTcs<g|]4}dD]"}dD]}|||q$qqS)rErSr )rr(rr)) ambig_codonrAr r r3sz)list_ambiguous_codons..rF)r0itemsrF) rRrAZc1_listZc2_listZc3_listZ candidatesr(rr)r+r'Zwantedr )rTrArRr r>s0         r>TGATAAZTRATAGZTARZUAGZUAAZUARc@s2eZdZdZddZddZd ddZd d ZdS) r=z@Forward table for translation of ambiguous nucleotide sequences.c Cs||_||_||_i}x>|jD]2\}}x(|D] }|j|i}d||<|||<q.Wq Wx |jD]\}}t|||<q`W||_i|_dS)zInitialize the class.rEN)rambiguous_nucleotideambiguous_proteinrUgetrG _inverted_cache) rrrYrZinvertedrCvalcrr r r rds  zAmbiguousForwardTable.__init__c Cs,y|j|dSttfk r&dSXdS)zCheck if codon works as key for ambiguous forward_table. Only returns 'True' if forward_table[codon] returns a value. TFN) __getitem__r&r)rr+r r r __contains__ws  z"AmbiguousForwardTable.__contains__Nc Cs$y |j|Stk r|SXdS)z,Implement get for dictionary-like behaviour.N)rar&)rr+failobjr r r r[s zAmbiguousForwardTable.getc syj|}Wntk r"Yn&X|tkr4t||tkrDt||Syj|}|j|<|Stk rtYnXyt|jj}WnJtk rtj|<t|Yn&tk rtj|<t|YnXt|dkstdt|dkr|dj|<|dSi}x8|D]0}x(j|D]}|j |dd||<q(WqWt|}g}x*|j D]\}}||krb|j |qbWt|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. rzunambiguous codons must coderEcstj||fS)N)lenrZ)r)rr r sz3AmbiguousForwardTable.__getitem__..)r2) r]r&rrrLrYrdAssertionErrorr\r[rUrFsort) rr+rrIZambiguous_possibler,Ztermnr_r )rr rasZ             z!AmbiguousForwardTable.__getitem__)N)rrrr rrbr[rar r r r r=as  r=cCs2dd|jddjddjdD}t|||g|||}t|tjtjtjtj }i} i} x8|j D],\} } | | | <| jdd} | | | <| | | <qdWg} g}x>|D]6} |j | d| kr| jdd} |j | | j | qWg}g}x@|D]8} |j | d| kr| jdd} |j | |j | qWt |||g| ||}t tjj }d|d<t|tj|tjtj }t|||g| | |}t|tjtjtjtj }|dkr|a|a|t|<|t|<|t|<|t|<|t|<|t|<|d k r|j |x>|D]6}|t|<|t|<|t|<|t|<|t|<|t |<qWd S) z_Turn codon table data into objects (PRIVATE). The data is stored in the dictionaries. cSsg|] }|jqSr )strip)rrr r r rsz'register_ncbi_table..z and z; z, rUrEN)!replacesplitr8r<r ambiguous_dnarambiguous_dna_valuesextended_proteinextended_protein_valuesrUrFr4dictambiguous_rna_valuesrNucleotideAlphabetr: ambiguous_rnastandard_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_namer r1rrr!dnaZ ambig_dnaZ rna_tableZ generic_tabler+r_Zrna_start_codonsZgeneric_start_codonsZrna_stop_codonsZgeneric_stop_codonsZgenericZ_merged_valuesZ ambig_genericrnaZ ambig_rnar r r register_ncbi_tables                 rStandardZSGC0rEFLSYCWPHQRIMrNKVADEG)=TTTTTCTTATTGTCTTCCTCATCGTATTACTGTTGCTGGCTTCTCCTACTGCCTCCCCCACCGCATCACCAACAGCGTCGCCGACGGATTATCATAATGACTACCACAACGAATAACAAAAAGAGTAGCAGAAGGGTTGTCGTAGTGGCTGCCGCAGCGGATGACGAAGAGGGTGGCGGAGGGrrr)rCrr r1rrzVertebrate MitochondrialZSGC1rS)rrrrrrrrrrrrrVrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrz`Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; SpiroplasmaZSGC3rzInvertebrate MitochondrialZSGC4z8Ciliate Nuclear; Dasycladacean Nuclear; Hexamita NuclearZSGC5)?rrrrrrrrrrrWrXrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrz0Echinoderm Mitochondrial; Flatworm MitochondrialZSGC8 zEuplotid NuclearZSGC9 z%Bacterial, Archaeal and Plant Plastid zAlternative Yeast Nuclear zAscidian Mitochondrial z"Alternative Flatworm Mitochondrial)?rrrrrrrrrrrWrrrVrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrzBlepharisma Macronuclear)>rrrrrrrrrrrXrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrzChlorophycean MitochondrialzTrematode Mitochondrialz"Scenedesmus obliquus Mitochondrial)=rrrrrrrrrrXrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrzThraustochytrium Mitochondrial)rrrrrrrrrrrWrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr)%r Bior Bio.AlphabetrBio.Datarr}rwr~rxrryrrzrr{rr|rurv Exceptionrobjectr r3r4r8r:r<rLr>rnrfrrr=rr r r r sh   d#<      xe