ó ž{Ic@sÛddlZddlZddlZddlZy eZWn1ek rmddlmZddlmZ nXdZ dZ dZ dZ defd„ƒYZd fd „ƒYZd ejfd „ƒYZd ed„ZdS(iÿÿÿÿN(tSet(t ImmutableSetis[&t]t TreeErrorcBseZRS((t__name__t __module__(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyR stNodeDatacBs#eZdZddddd„ZRS(sHStores tree-relevant data associated with nodes (e.g. branches or otus).gcCs(||_||_||_||_dS(N(ttaxont branchlengthtsupporttcomment(tselfRRR R ((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt__init__$s   N(RRt__doc__tNoneR (((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyR"stTreecBs¬eZdZd'dedeedd„Zd„Zd'd'd„Zd„Z d'd„Z d„Z d'd dd „Z d „Z d „Zd'd „Zd„Zd„Zd„Zd„Zd'd„Zed„Zd'd'd„Zd„Zd„Zed„Zd„Zd„Zd„Zd'd„Zd„Zd„Z d'd„Z!d'd'dd'ed„Z"d „Z#eeeed'd!„Z$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 Cs×tjj|ƒ||_||_||_||_||_||_tj |ƒƒ}|j |ƒ|j |_ |rÓ|j ƒjddƒjddƒ}|jdƒ}|jd|j d|j|ƒdƒndS( sNtree(self,tree).s Rs t;t parent_idttreeiN(tNodestChainR t dataclasst_Tree__values_are_supportt max_supporttweighttrootedtnametNodetaddtidtroottstriptreplacetrstript _add_subtreet_parse( R RRRRtdatatvalues_are_supportRR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyR 7s        $c Csg|jƒ}|jdƒ|jdƒkr=td|ƒ‚n|jdƒdkrH|jtƒ}|jdƒ}|dkr•|dkr•|d ggS|dkrÈ|dkrÈ|| |j||ƒgS|dkrÿ|dkrÿ|| |j||dƒgS||kr*|| |j||dƒgS|| |j||ƒgSn|jdƒ}|j||dƒ}|s€d g}ng}d}d}xŽtd|ƒD]}} || dkrÅ|d7}q¢|| dkrâ|d8}q¢|| dkr¢|dkr¢|j ||| !ƒ| d}q¢q¢W|j |||!ƒg|D]} |j | ƒ^q>} | |gSd S( sMParses (a,b,c...)[[[xx]:]yy] into subcomponents and travels down recursively.t(t)s'Parentheses do not match in (sub)tree: it:iÿÿÿÿit,N( R tcountRtfindtNODECOMMENT_STARTRt _get_valuestrfindtrangetappendR$( R Rt nodecommenttcolontclosingtvaltsubtreestpleveltprevtptsubtreet subclades((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyR$JsB      "cCsÆ|dkrtdƒ‚nx¤|D]œ}t|dƒtkrz|jƒ}t|ddtƒr‘|ddjtƒr‘|dj dƒ|_ nt |dƒdkrã|dd|_ |dddk rA|dd|_ qAn^t |dƒdkrA|js-|dddk r>|dd|_ q>qA|dd|_ ntj|ƒ}|j||ƒ|j|j|dƒq"|jƒ}t|ddtƒrÍ|ddjtƒrÍ|dj dƒ|_ n|d|_t |ƒdkrŸt |dƒdkr>|dd|_ |dddk rœ|dd|_ qœqŸt |dƒdkrŸ|jsˆ|dddk r™|dd|_ q™qœ|dd|_ qŸntj|ƒ}|j||ƒq"WdS(sKAdds leaf or tree (in newick format) to a parent_id. (self,parent_id,tree).sNeed node_id to connect to.iiiÿÿÿÿiN(RRttypetlistRt isinstancetstrt startswithR-tpopR tlenR RRRRRR#RR(R RRtsttndtsntleaf((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyR#tsF   .  .  cCs|dkrdSt|krÊ|jtƒ}|jtƒ}|dkr_tdttfƒ‚n|||d!}|| ||d}g|jdƒD]}|jƒr–t|ƒ^q–}|j|ƒn4g|jdƒD]}|jƒrÚt|ƒ^qÚ}|S(s9Extracts values (support/branchlength) from xx[:yyy], xx.Riÿÿÿÿs7Error in tree description: Found %s without matching %siR)N( RR-R,tNODECOMMENT_ENDRtsplitR tfloatR1(R ttexttnc_starttnc_endR2tttvalues((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyR.žs   44ccs]|dkr|j}nx>|j|ƒjD]*}|Vx|j|ƒD] }|VqFWq+WdS(s*Return all node_ids downwards from a node.N(RRtnodetsucct_walk(R ROtnRE((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyRQ±s   cCs-||jkr"td|ƒ‚n|j|S(sSReturn the instance of node_id. node = node(self,node_id) sUnknown node_id: %d(tchainR(R tnode_id((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyRO»sicCsº|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( RRRSR%R0RRRRR?RR1R(R RRRRtidst parent_datatiRO((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyRHÄs   cCs: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(RStitemsR%RR(R RRRO((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt search_taxonØscCsH|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( RYRRt get_terminalstunlinktkillRBRORPRRR%tcollapse(R RRR8RPtnew_bl((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytpruneâs"   ( cCsº|dkr|j}n||jkr:td|ƒ‚n|j|jgkr{|j|jrt|j|jjgSdSn;g}x.|j|jD]}|j|j|ƒƒq’W|SdS(svReturn a list of all otus downwards from a node (self, node_id). nodes = get_taxa(self,node_id=None) sUnknown node_id: %d.N( RRRSRRPR%Rtextendtget_taxa(R RTR=RP((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyRaÿs  cCs5g|jƒD]$}|j|ƒjgkr |^q S(s$Return a list of all terminal nodes.(tall_idsRORP(R RW((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyRZscCs|j|ƒjgkS(s(Returns True if node is a terminal node.(RORP(R RO((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt is_terminalscCst|j|ƒjƒdkS(s)Returns True if node is an internal node.i(RBRORP(R RO((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt is_internalscCsI|j|ƒrAtg|j|ƒjD]}|j|ƒ^q%kStSdS(s;Returns True if all successors of a node are terminal ones.N(RctFalseRORP(R RORR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytis_preterminal s2cCsM|dkr|j}ntg|j|ƒD]}|j|ƒr+|^q+ƒS(s@Counts the number of terminal nodes that are attached to a node.N(RRRBRQRc(R RORR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytcount_terminals&s  c CsMxFtrHx9|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( siCollapses all subtrees which belong to the same genus (i.e share the same first word in their taxon name.t t_iiRs RON( tTrueRQRcRaR!RHR1RBROR%RR\RP( R tspace_equals_underscoreRRttaxatgeneraRMtgenustknt nodes2kill((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytcollapse_genera,s.    % cCs‡|dkr|j}n|dkr3tdƒ‚nd}xG|dk r‚||k r‚||j|ƒjj7}|j|ƒj}q<W|S(s‹Adds up the branchlengths from root (default self.root) to node. sum = sum_branchlength(self,root=None,node=None) sMissing node id.gN(RRRROR%RR8(R RROtblen((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytsum_branchlengthJs   cCsä|j|ƒjgkr+|j|ƒjjSy6tg|j|ƒjD]}|j|ƒ^qDƒSWn||GH|j|ƒjGHx,|j|ƒjD]}|G|j|ƒGHqWg|j|ƒjD]}|j|ƒ^q¿GH‚nXdS(sWReturn subtree as a set of nested sets. sets = set_subtree(self,node) N(RORPR%Rt frozensett set_subtree(R RORR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyRuZs6-cCs"|j|jƒ|j|jƒkS(sXCompare tree and tree2 for identity. result = is_identical(self,tree2) (RuR(R ttree2((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt is_identicalmsc Cs t|jƒƒt|jƒƒ}t|jƒƒt|jƒƒ}|r­|sV|r­|rzddj|ƒ|jfGHn|ržddj|ƒ|jfGHntdƒ‚ng|jƒD]„}|j|ƒjrº|j|ƒjrº|j|ƒjj rº|j|ƒjj |krºt|j|ƒƒ|j|ƒjj f^qº}g|jƒD]„}|j|ƒjrQ|j|ƒjrQ|j|ƒjj rQ|j|ƒjj |krQt|j|ƒƒ|j|ƒjj f^qQ}g} x¸|D]°\} } x¡|D]™\} } | j | ƒ rû| j | ƒ rû| | @| | | | }}}|r”|j |ƒph|j |ƒ r”| j | | | | |||fƒq”qûqûWqèW| S(s‚Compares 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.( tsetRatjoinRRRbRORPR%R tissubsetR1(R Rvt thresholdtstricttmissing2tmissing1RRtt1tt2tconflicttst1tsup1tst2tsup2t intersecttnotin1tnotin2((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt is_compatiblets,""rr  %0cCse|jg|j|j|ƒ}|jg|j|j|ƒ}g|D]}||krE|^qEdS(syReturn the common ancestor that connects two nodes. node_id = common_ancestor(self,node1,node2) iÿÿÿÿ(Rttrace(R tnode1tnode2tl1tl2RR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytcommon_ancestor“scCs2|j||ƒ}|j||ƒ|j||ƒS(sqAdd and return the sum of the branchlengths between two nodes. dist = distance(self,node1,node2) (RRs(R R‹RŒtca((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytdistancežscCs­t|tƒr!t|gƒ}n t|ƒ}|j}xpt|j|ƒƒ}||kr^|SxD|j|jD].}t|j|ƒƒj|ƒro|}PqoqoWdSq9WdS(s’Return node_id of common ancestor if taxon_list is monophyletic, -1 otherwise. result = is_monophyletic(self,taxon_list) iÿÿÿÿN(R>R?RxRRaRSRPt issuperset(R t taxon_listt taxon_setRTt subclade_taxatsubnode((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytis_monophyletic¦s   cCs$|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(RRRBRORPtis_bifurcatingRjRe(R RO((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyR˜¼s  -<cCsWxP|jjƒD]?}|j|ƒjj|j|ƒj_d|j|ƒj_qWdS(sæMove 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(RStkeysROR%RR (R RR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytbranchlength2supportÍs$cCsTxM|jƒD]?}|j|ƒjjr |j|ƒjjt|ƒ:_q q WdS(sÎConvert absolute support (clade-count) to rel. frequencies. Some software (e.g. PHYLIP consense) just calculate how often clades appear, instead of calculating relative frequencies.N(RQROR%R RI(R tnrepRR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytconvert_absolute_supportØscCs;x4|j|ƒD]}|j|ƒjjrtSqWtSdS(s:Returns True if any of the nodes has data.support != None.N(RQROR%R RjRe(R RORR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt has_supportâscCs£| r|rt|ƒ}n{| rY|rYgt|ƒD]}dt|dƒ^q6}n>| rv| rvtdƒ‚n!|t|ƒkr—tdƒ‚n|jƒ|jƒ}x­t|ƒ|kr\tj|ƒ}|jd|d|ƒ} |r?xM| D]B} tj ||ƒ} | dkr#d} n| |j | ƒj _ qöWn|j | ƒ|j|ƒq°Wtj|ƒx2t||ƒD]!\} } | |j | ƒj _qzWdS( s Generates a random tree with ntax taxa and/or taxa from taxlabels. new_tree = randomize(self,ntax=None,taxon_list=None,branchlength=1.0,branchlength_sd=None,bifurcate=True) Trees are bifurcating by default. (Polytomies not yet supported). Ris7Either numer of taxa or list of taxa must be specified.s-Length of taxon list must correspond to ntax.RRiN(RBR0R?RR RZtrandomtchoiceRHtgaussROR%RR`tremovetshuffletzipR(R tntaxR“Rtbranchlength_sdt bifurcateRWt terminalstnewsplitt new_terminalstnttblROR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt randomizeês0  0       c Cs€dg}x?|jƒD]1}|j|ƒ}|jst|jt|ƒd t|jƒt|jƒd d d d fƒq|jj}|sd }n|jj}|dkr¶d }d }n|j d |ƒ}|jj }|dkréd }n|jj }|dkr d }n|jt|ƒ|t|jƒt|jƒ||||fƒqWd j g|D]} d | ^qXƒGHd G|jGHdS(s#Quick and dirty lists of all nodes.t#RR8RPtbrlens blen (sum)R R t-ROs s$%3s %32s %15s %15s %8s %10s %8s %20ss Root: N(R­RR8RPR®s blen (sum)R R (RbROR%R1R?R8RPRRRRsR R RyR( R ttableRWRRttxtblengtht sum_blengthR R tl((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytdisplays,  @           A%c s|s |rt}n|ˆ_|ˆ_|ˆ_t‡fd†‰d‡fd†‰d‡‡‡‡fd†‰dg}ˆjr”|jˆjƒn |jdƒ|jdƒˆjdkré|jdtt t ˆjƒd ƒƒƒnˆj r|jd ƒnˆˆj ˆj ƒjƒ}g|D]}ˆ|d |ƒ^q$} |jd d j| ƒƒ|rj|dSdj|ƒdSdS(sReturn a paup compatible tree line. to_string(self,support_as_branchlengths=False,branchlengths_only=False,plain=True) csȈjr dSˆjr5|r'dˆjSd|jSnˆjrId|jS|rZd|jS|jdk rŒ|jdk rŒd|j|jfS|jdk r¦d|jS|jdk rÀd|jSdSdS( s/Creates nicely formatted support/branchlengths.Rs:%1.2fs:%1.5fs %1.2f:%1.5fs 0.00000:%1.5fs %1.2f:0.00000s 0.00:0.00000N(tplaintsupport_as_branchlengthsRR tbranchlengths_onlyRR(R%tterminal(R (s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytmake_info_string5s"        cs’|dkrˆg|D]}ˆjd|ƒ|f^q}|jƒ|dksY|dkrf|jƒn|rt|Œd}qŽg}n|}|S(s=Sorts node numbers according to the number of terminal nodes.tlefttLEFTtrighttRIGHTROi(R»R¼R½R¾(RgtsorttreverseR£(tnodest ladderizeRRtsuccnode_terminalst succnodes(R (s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytladderize_nodesMs +   cs±ˆj|ƒjsAˆj|ƒjjˆˆj|ƒjdtƒSˆˆj|ƒjd|ƒ}g|D]}ˆ|d|ƒ^qf}ddj|ƒˆˆj|ƒjƒfSdS(s1Convert a node tree to a newick tree recursively.R¹RÂs(%s)%sR*N(RORPR%RRjRy(RORÂRÄRER6(RÅRºt newickizeR (s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyRÆ\s /%Rta_treet=is[&W%s]is[&R]RÂs(%s)R*iÿÿÿÿRhRN(ReR·R¸R¶RRR1RR?troundRIRRORRPRy( R R·R¸R¶t plain_newickRÂttreelineRÄRER6((RÅRºRÆR s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt to_string)s.         , %cCs|jdtƒS(s.Short version of to_string(), gives plain treeR¶(RÌRj(R ((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt__str__xscsȇ‡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.csqg}xdˆj|ƒjD]P}|j||ˆj|ƒjjˆj|ƒjjgƒ|jˆ|ƒƒqW|S(N(RORPR1R%RR R`(ROtbranchestb(t _get_branchesR (s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyRÐs 7iiiis,Support mismatch in bifurcating root: %f, %fN( RtunrootedRBRORPRAtindexRR1RRI(R RÏt rootbranchestb1tb2t newbranch((RÐR s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytunroot|s$!/""# $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( Ncs#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 enumerateRÑRARtlinkROR%RR (tparenttchildRWtbranchRÏtchild_branchesRP(t_connect_subtreeR (s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyRÞ¡s ,   iÿÿÿÿis%Unrooted and rooted Tree do not matchiiR%igs&Isolated nodes in tree description: %sR*(RRR—RBRORPR×RØRÑR8RARRbRRRRRR1RyR\( R toutgroupt outgroup_nodeRWRÏt root_brancht ingroup_nodeRRRtoldroot((RÞR s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytroot_with_outgroupŸsD  K ,     'Fgà?c Csu|r|rtdƒ‚n|p$|s6tdƒ‚n|dkr»y`|j|jƒj}tg|D]!}t|j|ƒƒ|f^qdƒ}|j|dƒ}WqÈtdƒ‚qÈXn |j|ƒ|rét |d|d|ƒ}n&|j ƒs|j ƒn|j|ƒx_|j ƒD]Q}|j |j|ƒƒ} | dkr|j| ƒjj|j|ƒj_qqWdS( sïMerges clade support (from consensus or list of bootstrap-trees) with phylogeny. tree=merge_bootstrap(phylo,bs_tree=) or tree=merge_bootstrap(phylo,consree=consensus_tree with clade support) sASpecify either list of boostrap trees or consensus tree, not boths8Specify either list of boostrap trees or consensus tree.isError determining outgroup.R{RßiÿÿÿÿN(RRRORRPtminRBRaRät consensusRRšRQR—R%R ( R tbstreestconstreeR{RßRÄRRtsmallesttpnodetcnode((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pytmerge_with_supportãs*   4     N()RRR RReRR R$R#R.RQRORHRYR_RaRZRcRdRfRgRjRqRsRuRwR‰RR‘R—R˜RšRœRR¬RµRÌRÍR×RäRì(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyR*sF  **                 $ O  # Dgà?cs>t|ƒ}|dkrd S|dj}|dj}i}t|djƒƒ}d}xÔ|D]Ì} |d7}|t| jƒƒkr–tdƒ‚n| jd|ƒx‚| j| j ƒD]n} | j| ƒ} | j ƒt | ƒ} | |kr|| ct | j ƒ|7=threshold from a list of trees.iis.Trees for consensus must contain the same taxaRßRsconsensus_%2.1fR%cs2tˆj|ƒjjƒtˆj|ƒjjƒS(N(RBROR%R(txty(Ræ(s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyt:siÿÿÿÿscorrupt tree structure?N(RBRRRRxRaRRäRQRR¿R?RIRRXRRRR%R tevalRRRORbRØR’tsystexitRARÙ(ttreesR{RßttotalRRtcladestalltaxatcRMtst_nodeR•R9tsROt consensus_idsRWtcurrentRÚ((Ræs‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyRæsX             - !-(RñRžtcopyRRxt NameErrortsetsRRRttPRECISION_BRANCHLENGTHtPRECISION_SUPPORTR-RGt ExceptionRRRRRRæ(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Trees.pyts $   ÿÿß