Mercurial > repos > yufei-luo > s_mart

comparison commons/core/tree/Tree.py @ 6:769e306b7933

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Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 import os, re, sys
2
3 class Tree:
4
5 def __init__( self, inFileName="" ):
6 self.tree = None
7 self.inFileName = inFileName
8 if self.inFileName != "":
9 self.loadTree()
10
11 def loadTree( self, verbose=0 ):
12 inF = open( self.inFileName, "r" )
13 lines = inF.readlines()
14 inF.close()
15 line = "".join(lines).replace("\n","")
16 self.tree = self.parseTree( line )
17 if verbose > 0:
18 print "nb of leaves: %i" % ( self.getNbOfLeaves( self.tree ) )
19
20 def parseTree( self, sTree ):
21 if "," not in sTree:
22 name, length = sTree.split(":")
23 return self.makeLeaf( name, float(length) )
24
25 distPattern = re.compile(r'(?P<tree>\(.+\))\:(?P<length>[e\-\d\.]+)$')
26 m = distPattern.search( sTree )
27 length = 0
28 if m:
29 if m.group('length'): length = float( m.group('length') )
30 sTree = m.group('tree')
31 if length == "": length = 0
32
33 lhs, rhs = self.parseSubTree( sTree )
34
35 return { "name": "internal",
36 "left": self.parseTree( lhs ),
37 "right": self.parseTree( rhs ),
38 "length": length }
39
40 def makeLeaf( self, name, length ):
41 return { "left":None, "right":None, "name":name, "length":length }
42
43 def parseSubTree( self, sTree ):
44 """
45 Parse a newick-formatted string of type 'a,b' into [a,b]
46 """
47 chars = list( sTree[1:-1] )
48 count = 0
49 isLhs = True
50 leftS = ""
51 rightS = ""
52 for c in chars:
53 if c == "(":
54 count += 1
55 elif c == ")":
56 count -= 1
57 elif (c == ",") and (count == 0) and (isLhs) :
58 isLhs = False
59 continue
60 if isLhs: leftS += c
61 else: rightS += c
62 return [ leftS, rightS ]
63
64 def toNewick( self, tree ):
65 newString = ""
66 if tree["name"] is not "internal":
67 newString += tree["name"]
68 else:
69 newString += "("
70 newString += self.toNewick( tree["left"] )
71 newString += ","
72 newString += self.toNewick( tree["right"] )
73 newString += ")"
74 if tree["length"]:
75 newString += ":"
76 newString += "%f" % ( tree["length"] )
77 return newString
78
79 def saveTree( self, outFileName ):
80 outF = open( outFileName, "w" )
81 outF.write( self.toNewick( self.tree ) )
82 outF.close()
83
84 def replaceHeaderViaPrefixSearch( self, tree, dNew2Init ):
85 if dNew2Init.has_key( tree["name"] ):
86 tree["name"] = dNew2Init[ tree["name"] ].replace(" ","_").replace("::","-").replace(",","-")
87 if tree["left"] != None:
88 self.replaceHeaderViaPrefixSearch( tree["left"], dNew2Init )
89 if tree["right"] != None:
90 self.replaceHeaderViaPrefixSearch( tree["right"], dNew2Init )
91
92 def retrieveInitialSequenceHeaders( self, dNew2Init, outFileName ):
93 tree = self.tree
94 self.replaceHeaderViaPrefixSearch( tree, dNew2Init )
95 self.tree = tree
96 self.saveTree( outFileName )
97
98 def getNbOfChildNodes( self, tree, nbNodes ):
99 if tree["left"] is not None:
100 nbNodes += 1
101 nbNodes = self.getNbOfChildNodes( tree["left"], nbNodes )
102 if tree["right"] is not None:
103 nbNodes += 1
104 nbNodes = self.getNbOfChildNodes( tree["right"], nbNodes )
105 return nbNodes
106
107 def getNbOfNodes( self ):
108 nbNodes = 0
109 return self.getNbOfChildNodes( self.tree, nbNodes )
110
111 def getNbOfChildLeaves( self, tree, nbLeaves ):
112 if tree["name"] != "internal":
113 nbLeaves += 1
114 if tree["left"] is not None:
115 nbLeaves = self.getNbOfChildLeaves( tree["left"], nbLeaves )
116 if tree["right"] is not None:
117 nbLeaves = self.getNbOfChildLeaves( tree["right"], nbLeaves )
118 return nbLeaves
119
120 def getNbOfLeaves( self ):
121 nbLeaves = 0
122 return self.getNbOfChildLeaves( self.tree, nbLeaves )