ó Y_Sc@@sàdZddlmZmZddlZddlZddlmZejddkrpddl m Z e Z ndZ dZd Zd Zd efd „ƒYZd efd„ƒYZdejfd„ƒYZded„ZdS(sTree 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 (reroot trees, split terminal nodes). i(tabsolute_importtprint_functionNi(tNodesi(tzipis[&t]t TreeErrorcB@seZRS((t__name__t __module__(((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyR"stNodeDatacB@s#eZdZddddd„ZRS(sHStores tree-relevant data associated with nodes (e.g. branches or otus).gcC@s(||_||_||_||_dS(N(ttaxont branchlengthtsupporttcomment(tselfR R R R ((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt__init__(s   N(RRt__doc__tNoneR(((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyR&stTreecB@s¸eZdZd(dedeedd„Zd„Zd(d(d„Zd„Z d„Z d(d„Z d „Z d(d dd „Z d „Zd „Zd(d„Zd„Zd„Zd„Zd„Zd(d„Zed„Zd(d(d„Zd„Zd„Zed„Zd„Zd„Zd„Zd(d„Zd„Z d„Z!d(d„Z"d(d(dd(ed „Z#d!„Z$eeeed(ed"„Z%d#„Z&d$„Z'd(d%„Z(d(d(d&d(d'„Z)RS()swRepresents a tree using a chain of nodes with on predecessor (=ancestor) and multiple successors (=subclades). gð?tc C@sötjj|ƒ||_||_||_||_||_||_tj |ƒƒ}|j |ƒ|_ |rò|j ƒj ddƒj ddƒ}|jdƒ}|j|ƒ\} } |j|jg| gƒ|_|jd|jd| ƒndS(sNtree(self,tree).s Rs t;t parent_idttreeN(RtChainRt dataclasst_Tree__values_are_supportt max_supporttweighttrootedtnametNodetaddtroottstriptreplacetrstript_parset _add_nodedatatdatat _add_subtreetid( R RRRRR%tvalues_are_supportRRt subtree_infot base_info((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyR<s      $c C@sg|jƒ}|jdƒ|jdƒkr=td|ƒ‚n|jdƒdkrH|jtƒ}|jdƒ}|dkr•|dkr•|d ggS|dkrÈ|dkrÈ|| |j||ƒgS|dkrÿ|dkrÿ|| |j||dƒgS||kr*|| |j||dƒgS|| |j||ƒgSn|jdƒ}|j||dƒ}|s€d g}ng}d}d}xŽtd|ƒD]}} || dkrÅ|d7}q¢|| dkrâ|d8}q¢|| dkr¢|dkr¢|j ||| !ƒ| d}q¢q¢W|j |||!ƒg|D]} |j | ƒ^q>} | |gSd S( sMParses (a,b,c...)[[[xx]:]yy] into subcomponents and travels down recursively.t(t)s'Parentheses do not match in (sub)tree: it:iÿÿÿÿit,N( R tcountRtfindtNODECOMMENT_STARTRt _get_valuestrfindtrangetappendR#( R Rt nodecommenttcolontclosingtvaltsubtreestpleveltprevtptsubtreet subclades((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyR#PsB      "cC@sÆ|dkrtdƒ‚nx¤|D]œ}|jƒ}|j||ƒ}t|dtƒr’tj|ƒ}|j||ƒ|j |j |dƒq"|d|_ tj|ƒ}|j||ƒq"WdS(s4Adds leaf or tree (in newick format) to a parent_id.sNeed node_id to connect to.iN( RRRR$t isinstancetlistRRRR&R'R (R RRtsttndtsntleaf((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyR&ys    cC@sMt|ddtƒrG|ddjtƒrG|djdƒ|_n=t|ddtƒr„|dd|_|dd|d|j|ƒjD]*}|Vx|j|ƒD] }|VqFWq+WdS(s*Return all node_ids downwards from a node.N(RRtnodetsucct_walk(R RWtnRD((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyRY¾s   cC@s-||jkr"td|ƒ‚n|j|S(sKReturn the instance of node_id. node = node(self,node_id) sUnknown node_id: %d(tchainR(R tnode_id((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyRWÈsicC@sº|dkrtdƒ‚ng}|j|j}x‚t|ƒD]t}tjƒ}|r™|jƒ|_|jrŠ|jt |ƒ|j_n||j_ n|j |j ||ƒƒq>W|S(s‹Speciation: generates n (default two) descendants of a node. [new ids] = split(self,parent_id=None,n=2,branchlength=1.0): sMissing node_id.N( RRR[R%R4RRRR RFR R5R(R RRZR tidst parent_datatiRW((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyRKÑs   cC@s:x3|jjƒD]"\}}|jj|kr|SqWdS(s‹Returns the first matching taxon in self.data.taxon. Not restricted to terminal nodes. node_id = search_taxon(self,taxon) N(R[titemsR%R R(R R R'RW((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt search_taxonåscC@sH|j|ƒ}|dkr.td|ƒ‚n||jƒkrStd|ƒ‚nñ|j|ƒ}|j|ƒt|j|ƒjƒdkr@||j krÝ|j|j ƒjd|_ d|j|j ƒ_ |j|ƒq@|j|ƒjd}|j|ƒj j |j|ƒj j }|j |ƒ||j|ƒj _ n|SdS(s"Prunes 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' sTaxon not found: %ssNot a terminal taxon: %siigN( RaRRt get_terminalstunlinktkillRIRWRXRR R%tcollapse(R R R'R<RXtnew_bl((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytpruneïs"   ( cC@sº|dkr|j}n||jkr:td|ƒ‚n|j|jgkr{|j|jrt|j|jjgSdSn;g}x.|j|jD]}|j|j|ƒƒq’W|SdS(sfReturn a list of all otus downwards from a node. nodes = get_taxa(self,node_id=None) sUnknown node_id: %d.N( RRR[RRXR%R textendtget_taxa(R R\RARX((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyRi s  cC@s5g|jƒD]$}|j|ƒjgkr |^q S(s$Return a list of all terminal nodes.(tall_idsRWRX(R R_((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyRb!scC@s|j|ƒjgkS(s(Returns True if node is a terminal node.(RWRX(R RW((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt is_terminal%scC@st|j|ƒjƒdkS(s)Returns True if node is an internal node.i(RIRWRX(R RW((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt is_internal)scC@sI|j|ƒrAtg|j|ƒjD]}|j|ƒ^q%kStSdS(s;Returns True if all successors of a node are terminal ones.N(RktFalseRWRX(R RWRZ((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytis_preterminal-s2cC@sM|dkr|j}ntg|j|ƒD]}|j|ƒr+|^q+ƒS(s@Counts the number of terminal nodes that are attached to a node.N(RRRIRYRk(R RWRZ((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytcount_terminals4s  c C@sMxFtrHx9|jƒD]*}|j|ƒr1qn|j|ƒ}g}xo|D]g}|rn|jddƒ}ny|jddƒd}Wn d}nX||krM|j|ƒqMqMWt|ƒdkr|dd|j|ƒj _ g|jd|ƒD] }|^qú}x|D]}|j |ƒqWg|j|ƒ_ PqqWPqWdS( sjCollapses all subtrees which belong to the same genus (i.e share the same first word in their taxon name.)t t_iiRs RWN( tTrueRYRkRiR!RKR5RIRWR%R RdRX( R tspace_equals_underscoreRZttaxatgeneraRUtgenustknt nodes2kill((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytcollapse_genera:s.    % cC@s‡|dkr|j}n|dkr3tdƒ‚nd}xG|dk r‚||k r‚||j|ƒjj7}|j|ƒj}q<W|S(sƒAdds up the branchlengths from root (default self.root) to node. sum = sum_branchlength(self,root=None,node=None) sMissing node id.gN(RRRRWR%R R<(R RRWtblen((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytsum_branchlengthWs   c@sòˆj|ƒjgkr+ˆj|ƒjjSy*t‡fd†ˆj|ƒjDƒƒSWn–t|ƒtˆj|ƒjƒx7ˆj|ƒjD]#}td|ˆj|ƒfƒqŽWtgˆj|ƒjD]}ˆj|ƒ^q˃‚nXdS(sWReturn subtree as a set of nested sets. sets = set_subtree(self,node) c3@s|]}ˆj|ƒVqdS(N(t set_subtree(t.0RZ(R (sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pys qss%s %sN(RWRXR%R t frozensettprintR|(R RWRZ((R sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyR|gs* !2cC@s"|j|jƒ|j|jƒkS(sXCompare tree and tree2 for identity. result = is_identical(self,tree2) (R|R(R ttree2((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt is_identicalzscC@sªt|jƒƒt|jƒƒ}t|jƒƒt|jƒƒ}|r·|sV|r·|rtddj|ƒ|jfƒn|r¨tddj|ƒ|jfƒntdƒ‚ng|jƒD]„}|j|ƒjrÄ|j|ƒj rÄ|j|ƒj j rÄ|j|ƒj j |krÄt|j|ƒƒ|j|ƒj j f^qÄ}g|jƒD]„}|j|ƒjr[|j|ƒj r[|j|ƒj j r[|j|ƒj j |kr[t|j|ƒƒ|j|ƒj j f^q[}g} x¸|D]°\} } x¡|D]™\} } | j | ƒ r| j | ƒ r| | @| | | | }}}|rž|j |ƒpr|j |ƒ rž| j | | | | |||fƒqžqqWqòW| S(szCompares branches with support>threshold for compatibility. result = is_compatible(self,tree2,threshold) s'Taxon/taxa %s is/are missing in tree %sR.s6Can't compare trees with different taxon compositions.( tsetRiRtjoinRRRjRWRXR%R tissubsetR5(R R€t thresholdtstricttmissing2tmissing1RZtt1tt2tconflicttst1tsup1tst2tsup2t intersecttnotin1tnotin2((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt is_compatibles,""##rr  %0cC@se|jg|j|j|ƒ}|jg|j|j|ƒ}g|D]}||krE|^qEdS(sqReturn the common ancestor that connects two nodes. node_id = common_ancestor(self,node1,node2) iÿÿÿÿ(Rttrace(R tnode1tnode2tl1tl2RZ((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytcommon_ancestor scC@s2|j||ƒ}|j||ƒ|j||ƒS(sqAdd and return the sum of the branchlengths between two nodes. dist = distance(self,node1,node2) (R™R{(R R•R–tca((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytdistanceªscC@s³t|tƒr!t|gƒ}n t|ƒ}|j}xvtr®t|j|ƒƒ}||krd|SxD|j|jD].}t|j|ƒƒj|ƒru|}PququWdSq9WdS(sŠReturn node_id of common ancestor if taxon_list is monophyletic, -1 otherwise. result = is_monophyletic(self,taxon_list) iÿÿÿÿN( R@RFR‚RRrRiR[RXt issuperset(R t taxon_listt taxon_setR\t subclade_taxatsubnode((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytis_monophyletic²s    cC@s$|dkr|j}n||jkr t|j|ƒjƒdkr |j|j|ƒjdƒoŸ|j|j|ƒjdƒoŸ|j|j|ƒjdƒSt|j|ƒjƒdkrú|j|j|ƒjdƒoù|j|j|ƒjdƒSt|j|ƒjƒdkrtStSdS(s?Return True if tree downstream of node is strictly bifurcating.iiiiN(RRRIRWRXtis_bifurcatingRrRm(R RW((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyR¢Ès  -<cC@sQxJ|jD]?}|j|ƒjj|j|ƒj_d|j|ƒj_q WdS(såMove values stored in data.branchlength to data.support, and set branchlength to 0.0 This is necessary when support has been stored as branchlength (e.g. paup), and has thus been read in as branchlength. gN(R[RWR%R R (R RZ((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytbranchlength2support×s$cC@sTxM|jƒD]?}|j|ƒjjr |j|ƒjjt|ƒ:_q q WdS(sÆConvert absolute support (clade-count) to rel. frequencies. Some software (e.g. PHYLIP consense) just calculate how often clades appear, instead of calculating relative frequencies.N(RYRWR%R RL(R tnrepRZ((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytconvert_absolute_supportâscC@s;x4|j|ƒD]}|j|ƒjjrtSqWtSdS(s:Returns True if any of the nodes has data.support != None.N(RYRWR%R RrRm(R RWRZ((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt has_supportìscC@s£| r|rt|ƒ}n{| rY|rYgt|ƒD]}dt|dƒ^q6}n>| rv| rvtdƒ‚n!|t|ƒkr—tdƒ‚n|jƒ|jƒ}x­t|ƒ|kr\tj|ƒ}|jd|d|ƒ} |r?xM| D]B} tj ||ƒ} | dkr#d} n| |j | ƒj _ qöWn|j | ƒ|j|ƒq°Wtj|ƒx2t||ƒD]!\} } | |j | ƒj _qzWdS( sGenerates 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). R is7Either numer of taxa or list of taxa must be specified.s-Length of taxon list must correspond to ntax.RR iN(RIR4RFRRRbtrandomtchoiceRKtgaussRWR%R RhtremovetshuffleRR (R tntaxRR tbranchlength_sdt bifurcateR_t terminalstnewsplitt new_terminalstnttblRWR((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt randomizeôs0  0       c C@s•dg}xWt|jƒƒD]C}|j|ƒ}|jsz|jt|ƒd t|jƒt|jƒd d d d fƒq|jj}|s•d }nd |jj }|dkrÀd }d }nd |j d |ƒ}|jj }|dkr÷d }n d |}|jj }|dkr"d }n|jt|ƒ|t|jƒt|jƒ||||fƒqWtd jd „|Dƒƒƒtd|jƒdS(s#Quick and dirty lists of all nodes.t#R R<RXtbrlens blen (sum)R R t-s%0.2fRWs cs@s|]}d|VqdS(s$%3s %32s %15s %15s %8s %10s %8s %20sN((R}tl((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pys 4ss Root: %sN(RµstaxonsprevssuccR¶s blen (sum)ssupportscomment(tsortedRjRWR%R5RFR<RXR R RR{R R RRƒR( R ttableR_RZttxtblengtht sum_blengthR R ((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytdisplays0  @           *c @s‹|s |rt}n|ˆ_|ˆ_ˆˆ_|ˆ_t‡‡fd†‰d‡fd†‰d‡‡‡‡fd†‰dg}ˆjr |jˆjƒn |jdƒ|jdƒˆjdkrõ|jdt t t ˆjƒd ƒƒƒnˆj r|jd ƒnˆˆj ˆjƒjƒ}g|D]} ˆ| d |ƒ^q0} |jd d j| ƒƒ|rv|dSdj|ƒdSdS(s#Return a paup compatible tree line.c@s-ˆjrd}nëˆjrS|r1dˆj}qý|jrJd|j}qýd}nªˆjrld|j}n‘|r‚d|j}n{|jd k r¹|jd k r¹d|j|jf}nD|jd k rØd|j}n%|jd k r÷d|j}nd}ˆ r)t|d ƒr)t|j ƒ|}n|S( s/Creates nicely formatted support/branchlengths.Rs:%1.2fs:0.00s:%1.5fs %1.2f:%1.5fs 0.00000:%1.5fs %1.2f:0.00000s 0.00:0.00000R6N( tplaintsupport_as_branchlengthsRR tbranchlengths_onlyR RthasattrRFR6(R%tterminalt info_string(tignore_commentsR (sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytmake_info_stringAs,      c@sy|dkrot‡fd†|Dƒƒ}|dks@|dkrM|jƒn|rft|Œd}qug}n|}|S(s=Sorts node numbers according to the number of terminal nodes.tlefttLEFTtrighttRIGHTc3@s'|]}ˆjd|ƒ|fVqdS(RWN(Ro(R}RZ(R (sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pys bsi(sleftRÈsrightRÊ(R¹treverseR(tnodest ladderizetsuccnode_terminalst succnodes(R (sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytladderize_nodes_s   c@s±ˆj|ƒjsAˆj|ƒjjˆˆj|ƒjdtƒSˆˆj|ƒjd|ƒ}g|D]}ˆ|d|ƒ^qf}ddj|ƒˆˆj|ƒjƒfSdS(s1Convert a node tree to a newick tree recursively.RÃRÍs(%s)%sR.N(RWRXR%R RrRƒ(RWRÍRÏRDR:(RÐRÆt newickizeR (sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyRÑms /%Rta_treet=is[&W%s]is[&R]RÍs(%s)R.iÿÿÿÿRpRN(RmRÀRÁRÅR¿RRR5RRFtroundRLRRWRRXRƒ( R RÀRÁR¿t plain_newickRÍRÅttreelineRÏRDR:((RÅRÐRÆRÑR sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt to_string7s0          , %cC@s|jdtƒS(s.Short version of to_string(), gives plain treeR¿(R×Rr(R ((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt__str__‰sc@sȇ‡fd†‰ˆˆjƒˆ_tˆjˆjƒjƒdkrÄgˆjD]}ˆj|d krO|^qO}ˆjjˆjj|dƒƒ}ˆjjˆjj|dƒƒ}|d|d|d|dg}|ddkrÿ|j|dƒn²|ddkr#|j|dƒnŽ|d|dkrK|j|dƒnf|ddksk|ddkr‡|j|d|dƒn*t dt |dƒt |dƒfƒ‚ˆjj|ƒndS(s?Defines a unrooted Tree structure, using data of a rooted Tree.c@sqg}xdˆj|ƒjD]P}|j||ˆj|ƒjjˆj|ƒjjgƒ|jˆ|ƒƒqW|S(N(RWRXR5R%R R Rh(RWtbranchestb(t _get_branchesR (sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyRÛ’s 7iiiis,Support mismatch in bifurcating root: %f, %fN( RtunrootedRIRWRXRHtindexRR5RRL(R RÚt rootbranchestb1tb2t newbranch((RÛR sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytunroots$!/""# $c @s¥‡‡fd†‰|dkr%ˆjSˆj|ƒ}|dkrDdStˆjˆjƒjƒdkr€|ˆjˆjƒjks|ˆjkr–ˆjSˆjƒxktˆjƒD]N\}}||d kr°ˆj|ƒj |d kr°ˆjj |ƒ}Pq°q°Wt dƒ‚||dkr+|d}n |d}x8ˆj ƒD]*}dˆj|ƒ_ gˆj|ƒ_qBWt jdtƒƒ}ˆj|ƒ|jˆ_ˆjj|j||d|dgƒˆjj|j|d d gƒˆ|j|ƒˆ|j|ƒgˆj ƒD]3}ˆj|ƒj dkr|ˆjkr|^q} t| ƒdkrxt d d j| ƒƒ‚n&t| ƒdkržˆj| dƒnˆjS( Nc@s#xitˆjƒD]B\}}||d kr||d krˆjj|ƒ}PqqWtd||fƒ‚ˆj||ƒ|dˆj|ƒj_|dˆj|ƒj_gˆjD]}||d kr¸|^q¸}xB|D]:}||dkr|d}n |d}ˆ||ƒqáWdS(s0Hook subtree starting with node child to parent.isFUnable to connect nodes for rooting: nodes %d and %d are not connectediiiN( t enumerateRÜRHRtlinkRWR%R R (tparenttchildR_tbranchRÚtchild_branchesRX(t_connect_subtreeR 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outgroup.R…RêiÿÿÿÿN(RRRWRRXtminRiRït consensusR¦R£RYR¡R%R ( R tbstreestconstreeR…RêRÏtsmallesttpnodetcnode((R sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytmerge_with_supportôs*        N(*RRRRRmRRR#R&R$R2RYRWRKRaRgRiRbRkRlRnRoRrRyR{R|RR“R™R›R¡R¢R£R¥R¦R´R¾R×RØRâRïR÷(((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyR/sH  )                  $ R  # Dgà?c@st|ƒ}|dkrd S|dj}|dj}i}t|djƒƒ}d}xÐ|D]È} |d7}|t| jƒƒkr–tdƒ‚n| jd|ƒx~| j| j ƒD]j} t | j| ƒƒ} t | ƒ} | |kr || ct | j ƒ|7=threshold from a list of trees.iis.Trees for consensus must contain the same taxaRêiRsconsensus_%2.1fR%c@s2tˆj|ƒjjƒtˆj|ƒjjƒS(N(RIRWR%R (txty(Rñ(sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pytIsiÿÿÿÿscorrupt tree structure?s&FATAL ERROR: consensus tree is corruptN(RIRRRR‚RiRRïRYRR¹RFRLRR`RÔRRRR%R tevalR RRWRjtsortRãRœRHRä(ttreesR…RêttotalRRtcladestalltaxatcRUtst_nodeRŸR=t delcladestsRWt consensus_idsR_tcurrentRå((RñsE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyRñsZ         :    - !-(Rt __future__RRR§tsysRRt version_infotfuture_builtinsRtxrangeR4tPRECISION_BRANCHLENGTHtPRECISION_SUPPORTR1RJt ExceptionRtobjectRRRRRñ(((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Trees.pyt s"    ÿÿë