瞤d; VdZddlmZddlZddlmZddlmZddlm Z ddl m Z m Z dd l mZmZmZmZ dd lmZd Zn #e$rd ZYnwxYwGd dZdZejddeee jdd Dze_dS)zw this module defines the evolutionary Model that can be linked to phylogeny, and computed by one of codeml, gerp, slr. )absolute_importN)range)sub)warn)PARAMSAVAIL) parse_paml parse_rst get_ancestor parse_slr)SequencePlotFaceTFcTeZdZdZddZdZdZdZdZ dd Z dd Z ddZ dZ dS)ModelaDEvolutionary model. "omega" stands for starting value of omega, in the computation. As Zihen Yang says, it is good to try with different starting values... model linked to tree by _tree variable results of calculation are stored in dictionaries: * branches: w dN dS bL by mean of their node_id * sites : values at each site. * classes : classes of sites and proportions * stats : lnL number of parameters kappa value and codon frequencies stored here. available models are: =========== ============================= ================== Model name Description Model kind =========== ============================= ================== %s =========== ============================= ================== :argument model_name: string with model name. Add a dot followed by anything at the end of the string in order to extend the name of the model and avoid overwriting. :argument None tree: a Tree object :argument None path: path to outfile, were model computation output can be found. Nc l||_t|\|_}d|_d|_d|_i|_i|_i|_t| D]\}}||j|<tttj }| |t| D])\} } | |vrtd| z| dkr| } | || <*||r||dSdS)Nz0WARNING: unknown param %s, can cause problems...gappy)_tree check_namenamesitesclasses n_classesbranchesstats propertieslistitemsdictr_change_paramsr_Model__check_marks_load) self model_nametreepathkwargsargsabparamskeyargs /lib/python3.11/site-packages/ete3/evol/model.py__init__zModel.__init__Qs@ $Z00 4    && $ $DAq"#DOQ  d6<>>**++ F###V\\^^,,  HC&  G#NOOOg~~gF3KK    JJt       cd}d}t|jD]\}}|r/|||j|jdd|j|jpdfzz }H|||j|jd|j|jdd|j|jpdfzz }d}d}|jrbd t|jDD]C||d fd t|jDfzz }Dd |jd d|j vr|j nddd|j vr|j ndd|jrFd tt|jndd|jr|ndd|jr|ndd S)z$ to print nice info z: mark:%-5s, omega: %-10s, node_ids: %-4s, name: %smarkNoneROOTwEDGEz %-12s: %s cg|]}|Sr8).0ts r- z!Model.__str__..{s666Aa666r/ c6g|]\}}d|d|dS)r=9r8)r9jir:s r-r;z!Model.__str__..|sJ5Q5Q5Q9=AEFaDD!!!QQQ5O5Q5Q5Qr/z Evolutionary Model z!: log likelihood : lnLz number of parameters : npz sites inference : z, z sites classes : z branches : z ) enumeratertraverseis_rootrnode_idrgetrsortedjoinrrBrCrrkeys)r"str_markstr_linerAnodestr_siter:s @r-__str__z Model.__str__hs8P !4!4!6!677 K KGAt||~~ KH dl(CF(K(.(, di6I6(KKKH dl(CF(K(, dl(C(G(GHN)P)P(, di6I6(KKK) < 366 !5!5666 3 3H3885Q5Q5Q5Q5>t|A5O5O5Q5Q5Q,2,2(333yyy DJ..txxF::DJ..twwF::>BjTtyyTZ__%6%6 7 788999fTT<3xxV33=4xxf44  r/ctd|jD}t|jD]o\}}|r&|jdrd|jpdi|j|j<-d|jdvr"ddt|zi|j|j<^ddi|j|j<pd S) zn checks if tree is marked and if model allows marks. fill up branches dict with marks cg|] }|j Sr8)r2)r9ns r-r;z'Model.__check_marks..sFFF1FFFr/ allow_markr2z #0branchtypz #r1N) anyriter_descendantsrDrErr2rrGstr)r"has_markrArNs r- __check_markszModel.__check_markss FF (C(C(E(EFFFGG !4!4!6!677 ; ;GAt ;DOL9 ;/5ty7IE.J dl++T_U333/5tCFF{.C dl++/5rl dl++ ; ;r/cj|jddkrt||d|jdvr8tjt |D]\}}t |||d|jdvrt |||jdt|d<|jdt|d<d S|jddkr^tjt|D]\}}t |||d t|d<d t|d<d Sd S) z9 parse outfiles and load in model object execcodemlsiterVancestorrBrCSlrrN) rr six iteritemsr setattrr rvarsr )r"r%r+vals r-r!z Model._loads@ ?6 "h . . tT " " "/// # ioo > >,,HCD#s++++T_U333T4(((!%U!3DJJ !%T!2DJJ    _V $ - -M)T*:*:;; ) )SsC((((!"DJJ !"DJJ    . -r/cJ|jdD] \}}|||< ||jd<dS)z. change model specific values changesr*N)r)r"r*r+changes r-rzModel._change_paramss; ?I6 ! !KC F3KK%+"""r/Tg?g333333?barFc |jtd|jzdSd|vr d|jz|d<d|jvrd}nd|jvrd}nd}|||}d |vrd |d <|r!|j|d d}t ri t |j|d f|||d |d|}n#t$rtdwxYw|rt|ddnt|ddnd}||j d<dS)a- To add histogram face for a given site mdl (M1, M2, M7, M8) can choose to put it up or down the tree. 2 types are available: * stick: to draw histogram. * curve: to draw plot. You can define color scheme by passing a diccionary, default is: col = {'NS' : 'grey' , 'RX' : 'green' , 'RX+': 'green' , 'CN' : 'cyan' , 'CN+': 'blue' , 'PS' : 'orange', 'PS+': 'red' } NzWARNING: model %s not computed.headerz$Omega value for sites under %s modelBEBNEBSLR)colylim)rrser5u Omega (ω))hlinescolorserrorsylabelkindzEERROR: no sites to display, only available histfaces for site models upTFhistface) rrr colorize_rstrHTREEVIEWrKeyError Exceptionrdr) r"ryrtrxrvrur&rfhists r- set_histfacezModel.set_histfaces" :  2di@ A A A46!!E $  +F8  DJ  CC dj CCC""3F"33#F6N  5Z_((t44F   ?' 3(<2V/5f/@t22+122 ? ? ?!>??? ? +dD))))dE****D&* ###s $B<<Cc:d}d|jvr|jd}nd}dD]-}||d|t|jd|dz }.|dz }tt|jdd D]f}|dvrt|jd|d r;||d|t|jd|dz }g||St |d |d S) z generate ctrl string to write to a file, if file is given, write it, otherwise returns the string :argument None outfile: if a path is given here, write control string into it. :returns: the control string r1sepz = )seqfiletreefileoutfilez>15r* cHtdd|S)Nfix_r1)rlowerxs r-z'Model.get_ctrl_string..sfb!''))44r/)r+*Nr5)rrYrIrrK startswithopenwrite)r"rstringrprms r-get_ctrl_stringzModel.get_ctrl_stringsm DO # #/5)CCC5 K KC ccc33&)$/(*CC*H&I&I&I&IK KFF$$t9>>@@AAH5H5666 P PC8884?H-c233>>sCC P###ss*-dox.H.M*N*N*N*NPP ?M #   $ $V , , , , ,r/cp ddddddddd|jd vrtd ||}fd |DS) al Colorize function, that take in argument a list of values corresponding to a list of classes and returns a list of colors to paint histogram. :param val: type of estimation, can be BEB or NEB (only positive-selection models have BEB) :param None col: a dictionary of colors that by default is: {"NS" : "grey", "RX" : "green", "RX+": "green", "CN" : "cyan", "CN+": "blue", "PS" : "orange", "PS+": "red"} :returns: a list of colors dependending categories of sites that are among: - CN+ > 0.99 probabylity of beloging to conserved class of site - CN > 0.95 probabylity of beloging to conserved class of site - NS not significant - RX+ > 0.99 probabylity of beloging to relaxed class of site - RX > 0.95 probabylity of beloging to relaxed class of site - PS+ > 0.99 probabylity of beloging to positively-selected class of site - PS > 0.95 probabylity of beloging to positively-selected class of site greygreencyanblueorangered)NSRXRX+CNCN+PSPS+r_rVz:ERROR: histogram are only for site and branch-site models.c g|] }| Sr8r8)r9catrqs r-r;z&Model.colorize_rst..7s///SC///r/)rr~significance_by_site)r"rfrq categoriess ` r-r{zModel.colorize_rsts4$V$$##%" $$///233 3..s33 ////J////r/cHd|jdvrtdd|jdv}g}t|j|d|j|dD]>\}}|dkr|d "||j|kr4|s2|d kr|d Q|d g|d kr2|d kr|d|d||j|kr4|r2|d kr|d|d||j|kr4|d kr|d |d )|d @|S)a Summarize significance of site models. :param val: type of estimation, can be BEB or NEB (only positive-selection models have BEB) :returns: a list of categories among: - CN+ > 0.99 probabylity of beloging to conserved class of site - CN > 0.95 probabylity of beloging to conserved class of site - NS not significant - RX+ > 0.99 probabylity of beloging to relaxed class of site - RX > 0.95 probabylity of beloging to relaxed class of site - PS+ > 0.99 probabylity of beloging to positively-selected class of site - PS > 0.95 probabylity of beloging to positively-selected class of site r_rVz,ERROR: only for site and branch-site models.positiveevolpvclassgffffff?rgGz?rrrrrr)rr~ziprappendr)r"rfps_modelrpval curr_classs r-rzModel.significance_by_site9s ///233 3!88 #DJsOD$9$(JsOG$<!>!> ( ( D*d{{!!$''''t~c22282$;;%%d++++%%e,,,,q$;;%%d++++%%e,,,,t~c222x2$;;%%d++++%%e,,,,t~c222$;;%%d++++%%e,,,,!!$''''r/)NN)TrjrkFN)N) __name__ __module__ __qualname____doc__r.rPr r!rrrr{rr8r/r-rr;s*.$ $ $ N ; ; ;###*,,,=B+/1+1+1+1+h!-!-!-!-F%0%0%0%0N/////r/rcrtdd|tvr|ttdd|fSdS)zC check that model name corresponds to one of the available z\..*r1N)rr )models r-rrks? 62u&&eSU33444'&r/rc vg|]6}dd|zddt|dddt|ddd7S) z z%s8z r27rV15z r )r9rs r-r;r;us^///!"#ajjjj%(6*:*:*:*:E!HUOOOOM///r/c(t|dS)NrVrrs r-rrws %ar/)r+reverse)r __future__rrb six.movesrrerwarningsr evol.controlrr evol.parserr r r r treeview.facesrr| ImportErrorrrrJrIrKr8r/r-rsP'&&&&& ((((((((IIIIIIIIIIII111111HHHHH mmmmmmmm` 555 //&,fVVJEJLL-A-AG0G0(,'.'.'.///001 s=AA