瞤dG\.dZddlmZddlmZddlmZddlmZm Z m Z ddl m Z dd l mZmZdd lmZdd lZdd lZdd lmZd ZdZdZdZdZ ddlmZdZn#e$r ddlmZYnwxYw ddlm Z dZ!n #e$rdZ!YnwxYwddgZ"dZ#GddeZ$e$Z%d S)z this module defines the EvolNode dataytype to manage evolutionary variables and integrate them within phylogenetic trees. It inheritates the coretype PhyloNode and add some speciall features to the the node instances. )absolute_import)which) translate)ModelPARAMSAVAIL) write_newick) PhyloNodeSeqGroup)warnN)mapzFrancois-Jose Serrazfrancois@barrabin.orgGPLv3z0.0a Yang, Z., Nielsen, R., Goldman, N., & Pedersen, A. M. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-49. Retrieved from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1461088&tool=pmcentrez&rendertype=abstract Yang, Z., & Nielsen, R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular biology and evolution 19: 908-17. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/12032247 Bielawski, J. P., & Yang, Z. 2004. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. Journal of molecular evolution 59: 121-32. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/15383915 Zhang, J., Nielsen, R., & Yang, Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular biology and evolution 22: 2472-9. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/16107592 Yang, Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular biology and evolution 24: 1586-91. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/17483113 )chi2c2dtj||z S)Nr)rcdf)xys 2lib/python3.11/site-packages/ete3/evol/evoltree.pychi_highrWsq48Aq>>11)r) TreeStyleTFEvolNodeEvolTreec|ddS)z; just to return specie name from fasta description Nnames r_parse_speciesr!es 8Orc (eZdZdZdddeddfdZdZdZd"d Zd Z d Z d Z d#dZ dZ e je deeejdd Ddeejfze _ d$fd Zd%fd Z d&fd Zd'dZdZdZd(dZexjeeejjddz c_d Zd'd!ZxZ S))ra Re-implementation of the standart TreeNode instance. It adds attributes and methods to work with phylogentic trees. :argument newick: path to tree in newick format, can also be a string :argument alignment: path to alignment, can also be a string. :argument fasta alg_format: alignment format. :argument sp_naming_function: function to infer species name. :argument format: type of newick format :argument binpath: path to binaries, in case codeml or SLR are not in global path. Nfastarc ,d|_|s4td}tj|d}||_i|_d|_tj |f|||d||r| | gdS)zM freebranch: path to find codeml output of freebranch model. z/tmp/ete3-tmp/ete3rF)newickformatsp_naming_functionN) workdirrospathsplitexecpath_models_EvolNode__gui_mark_moder __init___label_as_paml mark_tree) selfr' alignment alg_formatr)r(binpathkwargs ete3_paths rr1zEvolNode.__init__ys(  2f IgmmI..q1G  $4 Lv.@ L LDJ L L L  "    ! ! ! rrc||_dSNr0)r4vals r_set_mark_modezEvolNode._set_mark_modes"rc|jSr;r<)r4s r _is_mark_modezEvolNode._is_mark_modes ##rc|D]X}|r|dxxdz cc<|d|d||YdS)zS nid needs to be a list in order to keep count through recursivity rrnode_idN) get_childrenis_leaf add_feature_label_internal_nodes)r4nidnodes rrFzEvolNode._label_internal_nodess%%'' , ,D||~~  FFFaKFFF   YA / / /  & &s + + + +  , ,rcd}tttkr0fdD}td|t dD]}|d||dz }d||gdS)a to label tree as paml, nearly walking man over the tree algorithm WARNING: sorted names in same order that sequence WARNING: depends on tree topology conformation, not the same after a swap activates the function get_descendants_by_pamlid rcjg|]/}|dk-|0S)r)get_leaf_namescount).0nr4s r z+EvolNode._label_as_paml..sG555A$$&&,,Q//!33333rz(EvolTree require unique names for leavesc|jSr;rrs rz)EvolNode._label_as_paml..sqvr)keyrBN)lensetrK ExceptionsortedrErF)r4rGduplisleafs` rr2zEvolNode._label_as_pamls II#c$"5"5"7"78899 9 95555!4!4""555FFOO O4%5%5666  D   Y , , , 1HCC C((( ""C5)))))rc |D]}|j|kr|cS|j|kr|SdS#t$rtdYdSwxYw)zC returns node list corresponding to a given idname zNShould be first labelled as paml (automatically done when alignemnt is loaded)N)iter_descendantsrBAttributeErrorr)r4idnamerNs rget_descendant_by_node_idz"EvolNode.get_descendant_by_node_ids B**,,  9&&HHH'|v%% &% B B B A B B B B B B Bs$7 7AAct}|D]>}|j|j|j<|j|j|j<|j|j|j<?||ddS)z. to write algn in paml format pamloutfiler(N)r nt_sequenceid2seqrBr id2namename2idwrite)r4fullpath seq_grouprNs r _write_algnzEvolNode._write_algnsnJJ  2 2A*+-I QY '+,6I ai (() I af % %88888rTc ddlm}m}t||fi|}tj|j|j}t j d|z| |dz|j ddkr| |dzd n)| |dz|j d rd nd |d kr| |dz}n&t|dzd |t j} t j|tj|j|j d} || dg|||} n0#t$$r#t'd| wxYw| d\} } | t.jj} t j| | rt5d| zdS|rGt7|d| |tj|d|dSdS)a To compute evolutionnary models. e.g.: b_free_lala.vs.lele, will launch one free branch model, and store it in "WORK_DIR/b_free_lala.vs.lele" directory WARNING: this functionality needs to create a working directory in "rep" WARNING: you need to have codeml and/or SLR in your path The models available are: =========== ============================= ================== Model name Description Model kind =========== ============================= ================== %s =========== ============================= ================== **Note that M1 and M2 models are making reference to the new versions of these models, with continuous omega rates (namely M1a and M2a in the PAML user guide).** :argument model_name: a string like "model-name[.some-secondary-name]" (e.g.: "fb.my_first_try", or just "fb") * model-name is compulsory, is the name of the model (see table above for the full list) * the second part is accessory, it is to avoid over-writing models with the same name. :argument ctrl_string: list of parameters that can be used as control file. :argument True keep: links the model to the tree (equivalen of running `EVOL_TREE.link_to_evol_model(MODEL_NAME)`) :argument kwargs: extra parameters should be one of: %s. r)PopenPIPEz mkdir -p %sz/algnexecSlrz/tree ra allow_mark r$z/tmp.ctlwztmp.ctl)stdoutstdinstderrz1ERROR: {} not installed, or wrong path to binary  zERROR: inside codeml!! rrunoutN) subprocessrlrmrr+r,joinr*r systemrj propertiesrgget_ctrl_stringopengetcwdchdirr.OSErrorrVr( communicatedecodesysruencodingrsetattrlink_to_evol_model)r4 model_name ctrl_stringkeepr8rlrm model_objrhhlddirbin_procryerrs r run_modelzEvolNode.run_models6 +********d55f55 7<< in== -(*+++ G+,,,   '5 0 0 JJx/J = = = = JJx/%.%9,%GNrrQ  Q Q Q "  #33HZ4GHHKK *$c * * 0 0 = = = w||DM9+?+GHH H5$ *4#D222DD H H H9:@&,,HH H H##E**Sjj,--    +c1 2 2 21  N Iuc * * *  # #BGLL5$A$A9 M M M M M N Ns "E44-F! c vg|]6}dd|zddt|dddt|ddd7S) z z%s8z evol27typ15z r )rMrs rrOzEvolNode.sabbbGHqDAJJJJa 0 0 0 0%(5////Cbbbrc(t|dS)NrrrQs rrRzEvolNode.sSXYZS[\aSbr)rSreversez, r`c \tt|j|fd|i|d}|D]p}t t |j}|r||krtd|}t |j|_|rt|j|_qdS)a` same function as for phyloTree, but translate sequences if nucleotides nucleotidic sequence is kept under node.nt_sequence :argument alignment: path to alignment or string :argument alg_format: one of fasta phylip or paml :argument True alignment: set to False in case we want to keep it untranslated r6rz0WARNING: sequences with different lengths found!N) superrlink_to_alignment iter_leavesrTstrsequencerrcr) r4r5r6 nucleotidesr8 check_lenrYseq_len __class__s rrzEvolNode.link_to_alignment"s 0h/  Q Q;E QIO Q Q Q $$&& < |st}n|}|r|D]} ||}n"#t$rt d|zYnwxYwd|jvrWt |dkr0||dkr|dn||jdj r'|j |jdd|j |jddtt|||d St!d) aJ call super show of PhyloTree histface should be a list of models to be displayes as histfaces :argument layout: a layout function :argument None tree_style: tree_style object :argument Nonehistface: an histogram face function. This is only to plot selective pressure among sites model %s not computedhistfacerrFup)layout tree_styleTreeview module is disabledN)TREEVIEWrget_evol_modelr\rr~rTindex set_histfaceraligned_headeradd_face aligned_footrrshow ValueError)r4rr histfacestshistmdlrs rrz EvolNode.show9s  < [[ ;%;;D?"11$77)???4=>>>>>?%77y>>A--)//$2G2G12L2L,,,6666,,...~j14;)22N:6;;;;00N:6;;;; (D ! ! & &f & D D D D D:;; ;:AActr?|st}n|}|r|D]} || } n"#t$rt d| zYnwxYwd| jvrWt |dkr0|| dkr| dn| | jdj r'|j | jdd|j | jddtt||||||St!d) a  call super show adding up and down faces :argument layout: a layout function :argument None tree_style: tree_style object :argument Nonehistface: an histogram face function. This is only to plot selective pressure among sites rrrrFr)rrrthr)rrrr\rr~rTrrrrrrrrrenderr) r4 file_namerrtrrheaderrrrrrs rrzEvolNode.render]s  < [[ ;%;;D?"11$77)???4=>>>>>?%77y>>A--)//$2G2G12L2L,,,6666,,...~j14;)22N:6;;;;00N:6;;;;4((// &;=23q0:: ::;; ;rFc ddlm}ttt|}d|vrt|d}ndgt |z}|D]}t|ds|j|vrd|| |jvs+|d|| |j |rtd |j j z| d d || |jzd |jvr| d d dS) a function to mark branches on tree in order that paml could interpret it. takes a "marks" argument that should be a list of #1,#1,#2 e.g.: :: t=Tree.mark_tree([2,3], marks=["#1","#2"]) :argument node_ids: list of node ids (have a look to node.node_id) :argument False verbose: warn if marks do not correspond to codeml standard :argument kargs: mainly for the marks key-word which needs a list of marks (marks=['#1', '#2']) r)matchmarksz#1rB.z#[0-9]+Nz?WARNING: marks should be "#" sign directly followed by integer mark r$)rerlistrintrTtraversehasattrrBrrr3__doc__rEfeatures)r4node_idsverbosekargsrrrHs rr3zEvolNode.mark_trees C**++ e  w((EEF3x==(EMMOO - -D4++ |x''5 !=!=>>>E)t| < <=??BFGLSG137>3IJKKK  ChnnT\&B&B CCEEEEt},,  ,,, - -rct|trt|||}n|||j|jvr||jddtd|jvr0t|jdddzndz|_|j|jv|||j|j<tj |std|zdSt|jdkr+|j ddkr|d|d d Sd Sd S) a link EvolTree to evolutionary model * free-branch model ("fb") will append evol values to tree * Site models (M0, M1, M2, M7, M8) will give evol values by site and likelihood :argument path: path to outfile containing model computation result :argument model: either the name of a model, or a Model object (usually empty) __rrzERROR: not a file: rncodemlbLT)fillN) isinstancerr_loadr r/r-rr+r,isfilerrTr~change_dist_to_evol)r4r,models rrzEvolNode.link_to_evol_modelsW eS ! ! %t,,EE KK   jDL(())$//2S5:%%UZ%%d++A.//!33+,6.6..EJjDL(($) UZ w~~d##  &- . . .1 t|   ! !e&6v&>(&J&J  $ $T5t $ < < < < < " !&J&Jrcd |j|S#t$rtd|zYdSwxYw)z returns one precomputed model :argument modelname: string of the name of a model object stored :returns: Model object zERROR: Model %s not found.N)r/KeyErrorrV)r4 modelnames rrzEvolNode.get_evol_modelsQ B< * * B B B 2i@ A A A A A A Bs //rrc vddlm}t|dkr4dt|z}||ddt |dgd z }nDt|d kr|ddt |dgd }nt ||| }|%t |d ||S|S) z Inherits from Tree but adds the tenth format, that allows to display marks for CodeML. TODO: internal writting format need to be something like 0 r)subrpz %s 1 z\[&&NHX:mark=([ #0-9.]*)\]z\1rrs)rr(rrNrt)rrrrTr rrg)r4rrbr(rnwks rrgzEvolNode.writes  v;;"  s4yy)C 333U#DF8AFFFHH HCC [[B  #2E"46(1EEEGGCCthvFFFC   #   $ $S ) ) )JJrzargument formatzargument 10 formatc||}||}|j|jkrtddS t|drt|dr|j|jz dkrGt dt |j|jz zt|j|jz Std|j|j|j|jz fzdzdSd Sd S#t$r=td |j d |j d t|j j Yd SwxYw) ad Returns pvalue of LRT between alternative model and null model. usual comparison are: ============ ======= =========================================== Alternative Null Test ============ ======= =========================================== M2 M1 PS on sites (M2 prone to miss some sites) (Yang 2000). M3 M0 test of variability among sites M8 M7 PS on sites (Yang 2000) M8 M8a RX on sites?? think so.... bsA bsA1 PS on sites on specific branch (Zhang 2005) bsA M1 RX on sites on specific branch (Zhang 2005) bsC M1 different omegas on clades branches sites ref: Yang Nielsen 2002 bsD M3 different omegas on clades branches sites (Yang Nielsen 2002, Bielawski 2004) b_free b_neut foreground branch not neutral (w != 1) - RX if P<0.05 (means that w on frg=1) - PS if P>0.05 and wfrg>1 - CN if P>0.05 and wfrg>1 (Yang Nielsen 2002) b_free M0 different ratio on branches (Yang Nielsen 2002) ============ ======= =========================================== **Note that M1 and M2 models are making reference to the new versions of these models, with continuous omega rates (namely M1a and M2a in the PAML user guide).** :argument altn: model with higher number of parameters (np) :argument null: model with lower number of parameters (np) z7first model should be the alternative, change the orderg?lnLrrzS WARNING: Likelihood of the alternative model is smaller than null's (%f - %f = %f)z[ Large differences (> 0.1) may indicate mistaken assigantion of null and alternative modelsrzat least one of z or z, was not calculatedN) rnprrrrabsfloatrr exitget_most_likelyr)r4altnnulls rrzEvolNode.get_most_likelysP""4((""4(( 7TW   J K K K3 /tU## e(<(< 8dh&**#ADHtx,?(@(@$@$)$'DG*;$<$<>>>>!XtxDH1DAFFFFGGG 1     / / / D4999CG999N O O O %- . . . . . . /s A9C</C<$,777t|4T:DI I0IIA$$Qt|(DQ(GHHHH  I Irr;)r$T)r`T)NNN)NNNNNN)F)NNrr)!__name__ __module__ __qualname__rr!r1r>r@rFr2r^rjrsepr|rWr keysrr rrrr3rrrgrr replacerr __classcell__)rs@rrrls  #dw$210###$$$ , , , ,***( B B B 9 9 9?N?N?N?N@ C!) bbLRFSYSYZdZ_ZdZfZfSgSgncnc[_MaMaMabbb c c 44  && ' '  ))I$7=&*<<<<<<."<"<"<"<"<"rsP '&&&&&''''''''''((((((""""""""  " #   0       1111    $$$$$$HHHHH z "GIGIGIGIGIyGIGIGIV s$ A A$#A$(A11A;:A;