Mercurial > repos > yufei-luo > s_mart
view commons/core/tree/Tree.py @ 21:91f8c4ce8c27
Deleted selected files
author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:25:37 -0400 |
parents | 769e306b7933 |
children |
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import os, re, sys class Tree: def __init__( self, inFileName="" ): self.tree = None self.inFileName = inFileName if self.inFileName != "": self.loadTree() def loadTree( self, verbose=0 ): inF = open( self.inFileName, "r" ) lines = inF.readlines() inF.close() line = "".join(lines).replace("\n","") self.tree = self.parseTree( line ) if verbose > 0: print "nb of leaves: %i" % ( self.getNbOfLeaves( self.tree ) ) def parseTree( self, sTree ): if "," not in sTree: name, length = sTree.split(":") return self.makeLeaf( name, float(length) ) distPattern = re.compile(r'(?P<tree>\(.+\))\:(?P<length>[e\-\d\.]+)$') m = distPattern.search( sTree ) length = 0 if m: if m.group('length'): length = float( m.group('length') ) sTree = m.group('tree') if length == "": length = 0 lhs, rhs = self.parseSubTree( sTree ) return { "name": "internal", "left": self.parseTree( lhs ), "right": self.parseTree( rhs ), "length": length } def makeLeaf( self, name, length ): return { "left":None, "right":None, "name":name, "length":length } def parseSubTree( self, sTree ): """ Parse a newick-formatted string of type 'a,b' into [a,b] """ chars = list( sTree[1:-1] ) count = 0 isLhs = True leftS = "" rightS = "" for c in chars: if c == "(": count += 1 elif c == ")": count -= 1 elif (c == ",") and (count == 0) and (isLhs) : isLhs = False continue if isLhs: leftS += c else: rightS += c return [ leftS, rightS ] def toNewick( self, tree ): newString = "" if tree["name"] is not "internal": newString += tree["name"] else: newString += "(" newString += self.toNewick( tree["left"] ) newString += "," newString += self.toNewick( tree["right"] ) newString += ")" if tree["length"]: newString += ":" newString += "%f" % ( tree["length"] ) return newString def saveTree( self, outFileName ): outF = open( outFileName, "w" ) outF.write( self.toNewick( self.tree ) ) outF.close() def replaceHeaderViaPrefixSearch( self, tree, dNew2Init ): if dNew2Init.has_key( tree["name"] ): tree["name"] = dNew2Init[ tree["name"] ].replace(" ","_").replace("::","-").replace(",","-") if tree["left"] != None: self.replaceHeaderViaPrefixSearch( tree["left"], dNew2Init ) if tree["right"] != None: self.replaceHeaderViaPrefixSearch( tree["right"], dNew2Init ) def retrieveInitialSequenceHeaders( self, dNew2Init, outFileName ): tree = self.tree self.replaceHeaderViaPrefixSearch( tree, dNew2Init ) self.tree = tree self.saveTree( outFileName ) def getNbOfChildNodes( self, tree, nbNodes ): if tree["left"] is not None: nbNodes += 1 nbNodes = self.getNbOfChildNodes( tree["left"], nbNodes ) if tree["right"] is not None: nbNodes += 1 nbNodes = self.getNbOfChildNodes( tree["right"], nbNodes ) return nbNodes def getNbOfNodes( self ): nbNodes = 0 return self.getNbOfChildNodes( self.tree, nbNodes ) def getNbOfChildLeaves( self, tree, nbLeaves ): if tree["name"] != "internal": nbLeaves += 1 if tree["left"] is not None: nbLeaves = self.getNbOfChildLeaves( tree["left"], nbLeaves ) if tree["right"] is not None: nbLeaves = self.getNbOfChildLeaves( tree["right"], nbLeaves ) return nbLeaves def getNbOfLeaves( self ): nbLeaves = 0 return self.getNbOfChildLeaves( self.tree, nbLeaves )