o Rŀg=@sdZddlZddlZddlZddlmZdZdZdZdZ e de ed e e d Z Gd d d e ZGd ddZGdddejZdddZdS)aTree class to handle phylogenetic trees. Provides a set of methods to read and write newick-format tree descriptions, get information about trees (monphyly of taxon sets, congruence between trees, common ancestors,...) and to manipulate trees (re-root trees, split terminal nodes). N)Nodesz[&](|z|[(),])c@seZdZdZdS) TreeErrorz0Provision for the management of Tree exceptions.N)__name__ __module__ __qualname____doc__r r C/var/www/html/myenv/lib/python3.10/site-packages/Bio/Nexus/Trees.pyr src@seZdZdZdddZdS)NodeDatazGStore tree-relevant data associated with nodes (e.g. branches or otus).NcCs||_||_||_||_dS)zInitialize the class.N)taxon branchlengthsupportcomment)selfrrrrr r r__init__'s zNodeData.__init__)NrNN)r r r r rr r r rr$src@sleZdZdZddddeddfddZdd ZdOd d Zd d ZddZ dPddZ ddZ dQddZ ddZ ddZdPddZddZdd Zd!d"Zd#d$ZdPd%d&ZdRd(d)ZdOd*d+Zd,d-Zd.d/ZdRd0d1Zd2d3Zd4d5Zd6d7ZdPd8d9Zd:d;Zdd?Z     'dSd@dAZ!dBdCZ"   '   'dTdDdEZ#dFdGZ$dHdIZ%dPdJdKZ& dUdMdNZ'dS)VTreezmRepresent a tree using a chain of nodes with on predecessor (=ancestor) and multiple successors (=subclades).N?Fc Cstj|||_||_||_||_||_||_t |}| ||_ |rR| dd dd}|d}||\} } ||jg| g|_|j|j| ddSdS)zNtree(self,tree). r ;) parent_idtreeN)rChainr dataclass_Tree__values_are_support max_supportweightrootednameNodeaddrootstripreplacerstrip_parse _add_nodedatadata _add_subtreeid) rrr#r$r%r.values_are_supportr"r( subtree_info base_infor r rr;s    z Tree.__init__cs\|}|d|dkrtd||ddkr|t}|d}|dkr7|dkr7|dg}}||gS|dkrS|dkrS|d|||d}}||gS|dkrq|dkrq|d|||dd}}||gS||kr|d|||dd}}||gS|d|||d}}||gS|d}||dd}|sdg}g}d} d} d } t|d|} t | D]N\} }| s|dkr| d7} q|dkr| d8} q|tkrd } q|d kr| dkrt d d | d| dD}| || ||d} q|t krd } q| || |fdd|D}||gS)zVParse (a,b,c...)[[[xx]:]yy] into subcomponents and travels down recursively (PRIVATE).r)z'Parentheses do not match in (sub)tree: r:NrFT,css|]}t|VqdSN)len).0blkr r r zTree._parse..cg|]}|qSr )r,)r:subtreerr r zTree._parse..) r)countrfindNODECOMMENT_START _get_valuesrfind_re_block_delimiterssplit enumeratesumappendNODECOMMENT_END)rr nodecommentcolonbranchrclosingvalsubtreesplevelprev incommentblocksidxr;p subcladesr r@rr,Xsh     $ $     z Tree._parsecCs|durtd|D]8}|}|||}t|dtr2t|}|||||j |dq |d|_ t|}|||q dS)z=Add leaf or tree (in newick format) to a parent_id (PRIVATE).NzNeed node_id to connect to.r) rr r- isinstancelistrr&r'r/r0r)rrrstndsnleafr r rr/s     zTree._add_subtreecCst|ddtr|ddtr|dd|_nt|ddtr5|dd|_|ddd|d<t|dkr~t|ddkr[|dd|_|dddurY|dd|_ |St|ddkr~|j sw|ddduru|dd|_ |S|dd|_|S)zKAdd data to the node parsed from the comments, taxon and support (PRIVATE).rr6rN) r[str startswithrEpoprrr9rrr!)rr^r]r r rr-s$$  zTree._add_nodedatac Cs|dkrdSd}t|vr8|t}|t}|dkr"tdttf|||d}|d|||dd}g}d}dd|dDD]!}|rgz |t|WqFtyf|dusbJd |}YqFwqF|rp|d ||rw|||S) zBExtract values (support/branchlength) from xx[:yyy], xx (PRIVATE).rNr6z7Error in tree description: Found %s without matching %srcSsg|]}|qSr )r))r:tr r rrAsz$Tree._get_values..r5zTwo string taxonomies?r) rErDrMrrIrLfloat ValueErrorinsert)rtextrNnc_startnc_endvaluestaxonomypartr r rrFs<     zTree._get_valuesccs<|dur|j}||jD] }|V||EdHqdS)z4Return all node_ids downwards from a node (PRIVATE).N)r(nodesucc_walkrronr r rrqsz Tree._walkcCs ||jvr td||j|S)zKReturn the instance of node_id. node = node(self,node_id) zUnknown node_id: %d)chainr)rnode_idr r rros   z Tree.noderacCsz|durtdg}|j|j}t|D]&}t}|r1||_|jr-|jt||j_||j_ | | ||q|S)zSpeciation: generates n (default two) descendants of a node. [new ids] = split(self,parent_id=None,n=2,branchlength=1.0): NzMissing node_id.) rrtr.rangerr&r rrbrrLr')rrrsrids parent_datairor r rrIs   z Tree.splitcCs,|jD]\}}|jj|kr|SqdS)zReturn the first matching taxon in self.data.taxon. Not restricted to terminal nodes. node_id = search_taxon(self,taxon) N)rtitemsr.r)rrr0ror r r search_taxons  zTree.search_taxoncCs||}|durtd|||vrtd|||}||t||jdkrp||jkrN||jjd|_d||j_ |||S||jd}||j j ||j j }| ||||j _ |S)a!Prune a terminal taxon from the tree. id_of_previous_node = prune(self,taxon) If taxon is from a bifurcation, the connectiong node will be collapsed and its branchlength added to remaining terminal node. This might be no longer a meaningful value' NzTaxon not found: zNot a terminal taxon: rrr) r{r get_terminalsunlinkkillr9rorpr(rr.collapse)rrr0rUrpnew_blr r rprunes*          z Tree.prunecCs~|dur|j}||jvrtd||j|jgkr*|j|jr(|j|jjgSdSg}|j|jD] }|||q2|S)zfReturn a list of all otus downwards from a node. nodes = get_taxa(self,node_id=None) NzUnknown node_id: %d.)r(rtrrpr.rextendget_taxa)rrur\rpr r rr1s   z Tree.get_taxacsfddDS)z$Return a list of all terminal nodes.cs g|] }|jgkr|qSr rorpr:ryr@r rrAG z&Tree.get_terminals..)all_idsr@r r@rr|EszTree.get_terminalscCs||jgkS)z'Return True if node is a terminal node.rrror r r is_terminalIszTree.is_terminalcCst||jdkS)z(Return True if node is an internal node.r)r9rorprr r r is_internalMszTree.is_internalcs,|rdfdd|jDvSdS)z:Return True if all successors of a node are terminal ones.Fcr>r rr:rsr@r rrATrBz'Tree.is_preterminal..)rrorprr r@ris_preterminalQs zTree.is_preterminalcs*|durj}tfdd|DS)z?Count the number of terminal nodes that are attached to a node.Ncsg|] }|r|qSr rrr@r rrA\sz(Tree.count_terminals..)r(r9rqrr r@rcount_terminalsXszTree.count_terminalsTc Cs |D]f}||r q||}g}|D])}|r |dd}z |ddd}Wn ty5d}Ynw||vr?||qt|dkrk|dd||j _ t |j|d}|D]}| |q[g||_ nqd Sq) z|Collapse all subtrees which belong to the same genus. (i.e share the same first word in their taxon name.) T _rrNonez roN)rqrrr*rI IndexErrorrLr9ror.rr\r~rp) rspace_equals_underscorerstaxageneraregenus nodes2killknr r rcollapse_genera^s6          zTree.collapse_generacCsd|dur|j}|durtdd}|dur0||ur0|||jj7}||j}|dur0||us|S)zAdd up the branchlengths from root (default self.root) to node. sum = sum_branchlength(self,root=None,node=None) NzMissing node id.r)r(rror.rrU)rr(roblenr r rsum_branchlength}s zTree.sum_branchlengthc s|jgkr|jjSztfdd|jDWStyWt|t|j|jD]}t|d|q8tfdd|jDw)zWReturn subtree as a set of nested sets. sets = set_subtree(self,node) c3s|]}|VqdSr8 set_subtreerr@r rr<sz#Tree.set_subtree..rcr>r rrr@r rrArBz$Tree.set_subtree..)rorpr.r frozenset Exceptionprintrrrr r@rrs  zTree.set_subtreecCs||j||jkS)zXCompare tree and tree2 for identity. result = is_identical(self,tree2) )rr()rtree2r r r is_identicalszTree.is_identicalc s0tt}tt}|r>|s|r>|r,tdd|jf|r:tdd|jftdfddD}fddD}g}|D];\} } |D]4\} } | | s| | s| | @| | | | } }}| r||s||s|| | | | | ||fq`qZ|S)zyCompare branches with support>threshold for compatibility. result = is_compatible(self,tree2,threshold) z'Taxon/taxa %s is/are missing in tree %sr7z6Can't compare trees with different taxon compositions.cs`g|],}|jr.|jr.|jjr.|jjkrt||jjfqSr rorpr.rsetrr)r thresholdr rrAs   z&Tree.is_compatible..cs`g|],}|jr.|jr.|jjr.|jjkrt||jjfqSr rr)rrr rrAs   ) rrrjoinr%rrissubsetrL)rrrstrictmissing2missing1t1t2conflictst1sup1st2sup2 intersectnotin1notin2r )rrrr is_compatiblesV      zTree.is_compatiblecsB|jg||j|}|jg||j|fdd|DdS)zqReturn the common ancestor that connects two nodes. node_id = common_ancestor(self,node1,node2) csg|]}|vr|qSr r rl2r rrAz(Tree.common_ancestor..r6)r(trace)rnode1node2l1r rrcommon_ancestorszTree.common_ancestorcCs$|||}||||||S)zrAdd and return the sum of the branchlengths between two nodes. dist = distance(self,node1,node2) )rr)rrrcar r rdistances z Tree.distancecCs^t|}|j} t||}||kr|S|j|jD]}t|||r+|}nqdSq)zReturn node_id of common ancestor if taxon_list is monophyletic, -1 otherwise. result = is_monophyletic(self,taxon_list) Tr6)rr(rrtrp issuperset)r taxon_list taxon_setru subclade_taxasubnoder r ris_monophyleticszTree.is_monophyleticcCs|dur|j}||jkr7t||jdkr7|||jdo6|||jdo6|||jdSt||jdkrW|||jdoV|||jdSt||jdkrcdSdS)z?Return True if tree downstream of node is strictly bifurcating.NrrraTF)r(r9rorpis_bifurcatingrr r rrszTree.is_bifurcatingcCs6|jD]}||jj||j_d||j_qdS)zMove values stored in data.branchlength to data.support, and set branchlength to 0.0. This is necessary when support has been stored as branchlength (e.g. paup), and has thus been read in as branchlength. rN)rtror.rr)rrsr r rbranchlength2supports zTree.branchlength2supportcCs6|D]}||jjr||jj|_qdS)zConvert absolute support (clade-count) to rel. frequencies. Some software (e.g. PHYLIP consense) just calculate how often clades appear, instead of calculating relative frequencies. Nrqror.r)rnreprsr r rconvert_absolute_support$s zTree.convert_absolute_supportcCs(||D] }||jjrdSqdS)z9Return True if any of the nodes has data.support != None.TFrrrr r r has_support.s zTree.has_supportc Cs |s |r t|}n |s|rddt|D}n|s|std|t|kr)td||}t||krmt|}|j||d}|r]|D]} t||} | dkrUd} | | | j _ qG| || |t||ks7t|t||D] \} } | | | j _qwdS)aGenerate a random tree with ntax taxa and/or taxa from taxlabels. new_tree = randomize(self,ntax=None,taxon_list=None,branchlength=1.0,branchlength_sd=None,bifurcate=True) Trees are bifurcating by default. (Polytomies not yet supported). cSsg|] }dt|dqS)rr)rbrr r rrAFsz"Tree.randomize..z8Either number of taxa or list of taxa must be specified.z-Length of taxon list must correspond to ntax.)rrrN)r9rvrrr|randomchoicerIgaussror.rrremoveshufflezipr) rntaxrrbranchlength_sd bifurcate terminalsnewsplit new_terminalsntblror%r r r randomize6s4        zTree.randomizec Csdg}|D]m}||}|js'|t|dt|jt|jddddfq|jj}|s/d}|jjd}|dur>d}d}n|j |dd}|jj }|durQd}n|d}|jj }|dur_d}|t||t|jt|j||||fqt d dd|Dt d |jdS) z#Quick and dirty lists of all nodes.)#rrUrpbrlenz blen (sum)rr-z0.2fNrrcss|]}d|VqdS)z$%3s %32s %15s %15s %8s %10s %8s %20sNr )r:liner r rr<r=zTree.display..z Root: )rror.rLrbrUrprrrrrrrr() rtableryrstxblength sum_blengthrrr r rdisplay`sL  "  z Tree.displayc s|s|rd}|_|__|_dfdd dfdd dfdd d g}jr8|jn|d |d jd krV|d ttjddj r^|d j j }fdd|D} |dd | d|r|dSd |dS)z#Return a paup compatible tree line.Fcsjrd}nbjr!|rdjd}nU|jrd|jd}nJd}nGjr,d|jd}n<|r6d|jd}n2|jdurL|jdurL|jdd|jd}n|jdurYd|jd}n|jdurf|jdd}nd }sz t|j|}W|Sty~Y|Sw|S) z.Create nicely formatted support/branchlengths.rr5z1.2fz:0.00z1.5fNz0.00000:z:0.00000z 0.00:0.00000) plainsupport_as_branchlengthsr"rbranchlengths_onlyrrbrNAttributeError)r.terminal info_string)ignore_commentsrr rmake_info_strings:   z(Tree.to_string..make_info_stringNcs^|dvr+tfdd|D}|dks|dkr||r'tt|d}|Sg}|S|}|S)z.ladderize_nodes..rrr)sortedreverser\r)nodes ladderizesuccnode_terminals succnodesr@r rladderize_nodess z'Tree.to_string..ladderize_nodescsx|js|jj|jddS|jd}fdd|D}dd|d|jS) z1Convert a node tree to a newick tree recursively.T)rrcg|]}|dqSrr r:r_r newickizer rrArz5Tree.to_string..newickize..rr7r4)rorpr.rr)rorrrS)rrrrrrrs  "z!Tree.to_string..newickizera_tree=rz[&Wrrz[&R]crrr rrr rrArz"Tree.to_string..rr7r4r6rr)Fr8)rrrrr%rLr#roundrfr$ror(rpr) rrrr plain_newickrrtreelinerrSr )rrrrrrr to_strings0 %     zTree.to_stringcCs |jddS)z/Short version of to_string(), gives plain tree.T)r)rr@r r r__str__s z Tree.__str__csNfddj_tjjdkrfddjD}jj|d}jj|d}|d|d|d|dg}|dd urW||dnF|dd ure||dn8|d|dkru||dn(|ddks|ddkr||d|dntd t |dt |dfj|d Sd S) z>Define a unrooted Tree structure, using data of a rooted Tree.c sNg}|jD]}||||jj|jjg||q|Sr8)rorprLr.rrr)robranchesb _get_branchesrr rr sz"Tree.unroot.._get_branchesracs"g|] }j|ddvr|qSNra)r(r:rr@r rrAs"zTree.unroot..rrrNz,Support mismatch in bifurcating root: %f, %f) r(unrootedr9rorprdindexrLrrf)r rootbranchesb1b2 newbranchr rrunroots0   z Tree.unrootc sfdd|durjS|}|dkrdStjjdkr-|jjvs2|jkr5jStjD] \}}||ddvr^|j|ddvr^j |}nq>t d||dkrn|d}n|d} D]}d|_g|_qvt j td }||j_j|j||d|d gj|j|d d g|j||j|fd d  D} t| dkrt dd| t| dkr| djS)z5Define a tree's root with a reference group outgroup.cstjD]\}}||ddvr!|ddvr!j|}n qtd|f||dj_|dj_fddjD}|D]}|dkr[|d}n|d}|qNdS) z._connect_subtree..rr) rJr rdrlinkror.rr)parentrryrPchild_branchesrrp_connect_subtreerrrr!s(      z1Tree.root_with_outgroup.._connect_subtreeNr6raz%Unrooted and rooted Tree do not matchrrr.rrcs*g|]}|jdur|jkr|qSr8)rorUr(rr@r rrAds$z+Tree.root_with_outgroup..z$Isolated nodes in tree description: r7)r(rr9rorprrJr rUrdrrrr&rr'r0rLrr~) routgroup outgroup_noderyr root_branch ingroup_nodersr(oldrootr rrroot_with_outgroupsT  (            zTree.root_with_outgroup?c s|r|rtd|s|std|dur) or tree=merge_bootstrap(phylo,consree=consensus_tree with clade support) zBSpecify either list of bootstrap trees or consensus tree, not bothz9Specify either list of bootstrap trees or consensus tree.Nc3s"|] }t||fVqdSr8)r9rrr@r rr<s z*Tree.merge_with_support..rzError determining outgroup.)rrr6)rror(rpminrrr  consensusrrrqrr.r) rbstreesconstreerrrsmallestpnodecnoder r@rmerge_with_supportms4      zTree.merge_with_support)NNr8)Nrar)T)NNrNT)FFTFNT)NNr!N)(r r r r rrr,r/r-rFrqrorIr{rrr|rrrrrrrrrrrrrrrrrrrrrr r)r r r rr/sp   ?   !    :     *0 d (Prr!csXt|}|dkr dS|dj}|dj}i}t|d}|D]?}|t|kr.td|j|d||jD]$} t || } t | } | |vrW|| |j |7<q:|j ||| <q:q fdd| D} | D]} || =qmt dtd|d | D]\} } tj|d }| |j_tt| |j_|qdjj_|jj_}|jfd d d t|ddD]M\}}||ddD]}|jj|jjrnqtdt|jjdkr|jj|j_nd|j_||qd|dj_|tkr*tdS)zmCompute a majority rule consensus tree of all clades with relative frequency>=threshold from a list of trees.rNz.Trees for consensus must contain the same taxa)rcs"g|] \}}t|dkr|qS)r)r)r:crY)rr rrAszconsensus.. consensus_z2.1f)r%r.rcst|jjSr8)r9ror.r)x)r#r rszconsensus..)keyr6rzcorrupt tree structure?z&FATAL ERROR: consensus tree is corrupt)r9r r"rrrr rqr(rrbr#rzrrfrr&r.revalrr'rorsortrJrsysexitrdr)treesrrtotalr r"cladesalltaxarest_noder delcladesr*sro consensus_idsrycurrentrr )r#rrr#sn         r#)r!N)r rrer1rrPRECISION_BRANCHLENGTHPRECISION_SUPPORTrErMcompileescaperHrrrrrr#r r r rs,  k