ipyrad/analysis/tetrad.py
def _finalize_stats(self, ipyclient):
        """ write final tree files """

        ## print stats file location:
        #print(STATSOUT.format(opr(self.files.stats)))

        ## print finished tree information ---------------------
        print(FINALTREES.format(opr(self.trees.tree)))

        ## print bootstrap information --------------------------
        if self.params.nboots:
            ## get consensus, map values to tree edges, record stats file
            self._compute_tree_stats(ipyclient)
            ## print bootstrap info
            print(BOOTTREES.format(opr(self.trees.cons), opr(self.trees.boots))) 

        ## print the ASCII tree only if its small
        if len(self.samples) < 20:
            if self.params.nboots:
                wctre = ete3.Tree(self.trees.cons, format=0)
                wctre.ladderize()
                print(wctre.get_ascii(show_internal=True, 
                                      attributes=["dist", "name"]))
                print("")
            else:
                qtre = ete3.Tree(self.trees.tree, format=0)
                qtre.ladderize()
                #qtre = toytree.tree(self.trees.tree, format=0)
                #qtre.tree.unroot()
                print(qtre.get_ascii())
                print("")

        ## print PDF filename & tips -----------------------------
        docslink = "https://toytree.readthedocs.io/"    
        citelink = "https://ipyrad.readthedocs.io/tetrad.html"
        print(LINKS.format(docslink, citelink))
def _finalize_stats(self, ipyclient):
        """ write final tree files """

        ## print stats file location:
        #print(STATSOUT.format(opr(self.files.stats)))

        ## print finished tree information ---------------------
        print(FINALTREES.format(opr(self.trees.tree)))

        ## print bootstrap information --------------------------
        if self.params.nboots:
            ## get consensus, map values to tree edges, record stats file
            self._compute_tree_stats(ipyclient)
            ## print bootstrap info
            print(BOOTTREES.format(opr(self.trees.cons), opr(self.trees.boots))) 

        ## print the ASCII tree only if its small
        if len(self.samples) < 20:
            if self.params.nboots:
                wctre = ete3.Tree(self.trees.cons, format=0)
                wctre.ladderize()
                print(wctre.get_ascii(show_internal=True, 
                                      attributes=["dist", "name"]))
                print("")
            else:
                qtre = ete3.Tree(self.trees.tree, format=0)
                qtre.ladderize()
                #qtre = toytree.tree(self.trees.tree, format=0)
                #qtre.tree.unroot()
                print(qtre.get_ascii())
                print("")

        ## print PDF filename & tips -----------------------------
        docslink = "https://toytree.readthedocs.io/"    
        citelink = "https://ipyrad.readthedocs.io/tetrad.html"
        print(LINKS.format(docslink, citelink))
def _finalize_stats ( self , ipyclient ) : ## print stats file location: #print(STATSOUT.format(opr(self.files.stats))) ## print finished tree information --------------------- print ( FINALTREES . format ( opr ( self . trees . tree ) ) ) ## print bootstrap information -------------------------- if self . params . nboots : ## get consensus, map values to tree edges, record stats file self . _compute_tree_stats ( ipyclient ) ## print bootstrap info print ( BOOTTREES . format ( opr ( self . trees . cons ) , opr ( self . trees . boots ) ) ) ## print the ASCII tree only if its small if len ( self . samples ) < 20 : if self . params . nboots : wctre = ete3 . Tree ( self . trees . cons , format = 0 ) wctre . ladderize ( ) print ( wctre . get_ascii ( show_internal = True , attributes = [ "dist" , "name" ] ) ) print ( "" ) else : qtre = ete3 . Tree ( self . trees . tree , format = 0 ) qtre . ladderize ( ) #qtre = toytree.tree(self.trees.tree, format=0) #qtre.tree.unroot() print ( qtre . get_ascii ( ) ) print ( "" ) ## print PDF filename & tips ----------------------------- docslink = "https://toytree.readthedocs.io/" citelink = "https://ipyrad.readthedocs.io/tetrad.html" print ( LINKS . format ( docslink , citelink ) )
write final tree files
write final tree files