该文描述了一个Python脚本，用于处理CAFE（比较进化家庭扩展）软件的输出结果，比较在给定p值下任意两个节点间基因家族内的基因数目差异。脚本读取输入文件，解析树结构，找到目标节点，并分析其基因数量变化情况，如扩张、收缩和无变化等。此外，它还提供了一个示例输出，显示了不同节点之间的比较结果和统计信息。
cafe运行结果文件中，在给定p值的情况下比较任意两个节点的所有基因家族内的基因数目差异
注意：请在代码内部176行指定节点，以<XX>的格式，184行指定pvalue值
运行格式
python compare_GF_branch_geneNum.py report_run.cafe
结果形式：
<7>_vs_<19>: Expansion:10 Contraction:4 NoChange:2
输入文件head 20
Tree:(D20A:78.0334,(((D15A:42.0569,(D19A:24.509,D1A:24.509):17.5479):4.15507,(D8A:16.7282,(D5A:8.752,(D23A:7.71805,(D14A:4.17075,D13A:4.17075):3.5473):1.03395):7.97622):29.4837):26.7067,(D17A:63.6391,(D10A:24.4991,((D2A:5.87362,D4A:5.87362):15.5526,(D3A:14.2972,((D18A:5.4519,D16A:5.4519):4.97616,(D7A:8.67218,(D9A:7.36182,(D29A:5.72085,D24A:5.72085):1.64097):1.31036):1.75588):3.86919):7.12897):3.07286):39.14):9.2796):5.11474)
Lambda: 0.00345497
# IDs of nodes:(D20A<0>,(((D15A<2>,(D19A<4>,D1A<6>)<5>)<3>,(D8A<8>,(D5A<10>,(D23A<12>,(D14A<14>,D13A<16>)<15>)<13>)<11>)<9>)<7>,(D17A<18>,(D10A<20>,((D2A<22>,D4A<24>)<23>,(D3A<26>,((D18A<28>,D16A<30>)<29>,(D7A<32>,(D9A<34>,(D29A<36>,D24A<38>)<37>)<35>)<33>)<31>)<27>)<25>)<21>)<19>)<17>)<1>
# Output format for: ' Average Expansion', 'Expansions', 'No Change', 'Contractions', and 'Branch-specific P-values' = (node ID, node ID): (0,17) (2,5) (4,6) (3,9) (8,11) (10,13) (12,15) (14,16) (7,19) (18,21) (20,25) (22,24) (23,27) (26,31) (28,30) (29,33) (32,35) (34,37) (36,38)
# Output format for 'Branch cutting P-values' and 'Likelihood Ratio Test': (0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38)
Average Expansion: (-0.275867,-0.00123638) (-0.041496,-0.0156093) (-0.0156866,-0.0272004) (-0.0486825,-0.0353141) (-0.0294413,-0.00510007) (-0.034155,-0.00595008) (-0.0387914,-0.0144502) (-0.0107411,-0.0110502) (-0.13577,-0.094274) (-0.183989,-0.00378642) (-0.0863921,-0.00340005) (-0.0119002,-0.0105865) (-0.0730237,-0.012132) (-0.0656827,-0.00703191) (0.00100456,-0.00610463) (-0.0482188,-0.016382) (-0.043737,-0.0172321) (-0.0294413,-0.0185457) (-0.0284368,-0.0225639)
Expansion : (444,0) (165,39) (215,141) (7,102) (166,47) (105,15) (103,31) (115,100) (63,12) (147,121) (172,8) (110,106) (63,28) (134,14) (1040,140) (54,16) (133,19) (128,25) (99,67)
nRemain : (8012,12928) (11992,12656) (12250,12249) (12296,12188) (12090,12764) (12192,12835) (12221,12682) (12536,12513) (11049,11697) (10150,12608) (11263,12882) (12501,12547) (11867,12713) (11685,12826) (10781,12477) (12187,12681) (12048,12664) (12208,12677) (12184,12413)
nDecrease : (4485,13) (784,246) (476,551) (638,651) (685,130) (644,91) (617,228) (290,328) (1829,1232) (2644,212) (1506,51) (330,288) (1011,200) (1122,101) (1120,324) (700,244) (760,258) (605,239) (658,461)
'ID' 'Newick' 'Family-wide P-value' 'Viterbi P-values' 'cut P-value' 'Likelihood Ratio'
2 (D20A_82:78.0334,(((D15A_33:42.0569,(D19A_33:24.509,D1A_32:24.509)_32:17.5479)_31:4.15507,(D8A_26:16.7282,(D5A_26:8.752,(D23A_25:7.71805,(D14A_24:4.17075,D13A_25:4.17075)_25:3.5473)_25:1.03395)_25:7.97622)_26:29.4837)_31:26.7067,(D17A_19:63.6391,(D10A_24:24.4991,((D2A_23:5.87362,D4A_26:5.87362)_25:15.5526,(D3A_24:14.2972,((D18A_23:5.4519,D16A_26:5.4519)_26:4.97616,(D7A_27:8.67218,(D9A_26:7.36182,(D29A_27:5.72085,D24A_25:5.72085)_26:1.64097)_26:1.31036)_26:1.75588)_26:3.86919)_26:7.12897)_26:3.07286)_26:39.14)_30:9.2796)_33:5.11474)_35 0 ((7.634e-16,0.0588293),(0.448258,0.502734),(0.5804,0.911131),(0.746974,0.0381908),(0.875539,0.481526),(0.284329,0.576181),(0.79107,0.681889),(0.344421,0.718658),(0.466579,0.0326812),(0.00145406,0.185851),(0.392353,0.686762),(0.033923,0.195279),(0.637721,0.795835),(0.264531,0.686762),(0.00459271,0.753182),(0.723804,0.578845),(0.292717,0.578845),(0.795835,0.578845),(0.201943,0.403979))
4 (D20A_5:78.0334,(((D15A_14:42.0569,(D19A_7:24.509,D1A_10:24.509)_9:17.5479)_10:4.15507,(D8A_3:16.7282,(D5A_26:8.752,(D23A_11:7.71805,(D14A_6:4.17075,D13A_5:4.17075)_6:3.5473)_10:1.03395)_10:7.97622)_9:29.4837)_10:26.7067,(D17A_12:63.6391,(D10A_31:24.4991,((D2A_14:5.87362,D4A_3:5.87362)_14:15.5526,(D3A_35:14.2972,((D18A_20:5.4519,D16A_20:5.4519)_21:4.97616,(D7A_21:8.67218,(D9A_24:7.36182,(D29A_31:5.72085,D24A_28:5.72085)_27:1.64097)_24:1.31036)_23:1.75588)_23:3.86919)_23:7.12897)_21:3.07286)_21:39.14)_12:9.2796)_11:5.11474)_11 0 ((0.00717389,0.645638),(0.0317765,0.463194),(0.154706,0.296526),(0.613472,0.578316),(9.76727e-07,0.104013),(4.84155e-20,0.532826),(0.114966,1.24451e-06),(0.573495,0.111272),(0.576066,0.157901),(0.910632,4.69686e-05),(1.20375e-05,0.660967),(0.673466,7.74542e-18),(3.00582e-05,0.0952332),(5.01642e-09,0.671725),(0.355076,0.355076),(0.019872,0.570774),(0.128209,0.0394314),(0.786039,0.000120057),(0.00132197,0.208507))
7 (D20A_1:78.0334,(((D15A_5:42.0569,(D19A_0:24.509,D1A_2:24.509)_2:17.5479)_3:4.15507,(D8A_3:16.7282,(D5A_3:8.752,(D23A_2:7.71805,(D14A_0:4.17075,D13A_0:4.17075)_0:3.5473)_2:1.03395)_3:7.97622)_3:29.4837)_3:26.7067,(D17A_5:63.6391,(D10A_22:24.4991,((D2A_8:5.87362,D4A_6:5.87362)_8:15.5526,(D3A_38:14.2972,((D18A_10:5.4519,D16A_4:5.4519)_10:4.97616,(D7A_8:8.67218,(D9A_26:7.36182,(D29A_69:5.72085,D24A_25:5.72085)_26:1.64097)_24:1.31036)_16:1.75588)_16:3.86919)_16:7.12897)_14:3.07286)_14:39.14)_5:9.2796)_4:5.11474)_4 0 ((0.0322795,0.562461),(0.0724884,0.208789),(0.00437968,0.631433),(0.538998,0.700995),(0.631305,0.565268),(0.573507,0.0153174),(0.545049,5.68173e-05),(0.5,0.5),(0.347482,0.060019),(0.854415,6.85475e-07),(4.09087e-05,0.618035),(0.613475,0.00400401),(2.7214e-05,0.0522527),(5.43383e-21,0.631207),(0.635435,5.68355e-09),(3.04281e-08,0.550964),(1.49741e-09,4.65899e-15),(0.114045,0.00449171),(4.45526e-59,0.403979))
8 (D20A_0:78.0334,(((D15A_1:42.0569,(D19A_12:24.509,D1A_0:24.509)_6:17.5479)_6:4.15507,(D8A_35:16.7282,(D5A_47:8.752,(D23A_0:7.71805,(D14A_1:4.17075,D13A_40:4.17075)_21:3.5473)_21:1.03395)_24:7.97622)_24:29.4837)_6:26.7067,(D17A_1:63.6391,(D10A_13:24.4991,((D2A_8:5.87362,D4A_12:5.87362)_9:15.5526,(D3A_2:14.2972,((D18A_4:5.4519,D16A_15:5.4519)_7:4.97616,(D7A_7:8.67218,(D9A_9:7.36182,(D29A_6:5.72085,D24A_2:5.72085)_6:1.64097)_7:1.31036)_7:1.75588)_7:3.86919)_7:7.12897)_8:3.07286)_8:39.14)_5:9.2796)_5:5.11474)_5 0 ((0.000528388,0.576188),(0.000189648,0.721388),(3.7598e-05,1.81019e-07),(0.573495,1.2707e-15),(2.13668e-07,0.786039),(1.00806e-24,3.92353e-05),(3.7148e-35,0.660967),(1.52139e-36,9.92373e-26),(0.19546,0.624745),(0.00340247,0.0253595),(0.000526893,0.573493),(0.190861,0.000674858),(0.185568,0.226831),(2.3145e-06,0.565258),(9.17531e-05,9.06414e-12),(0.584096,0.523331),(0.647637,0.523331),(0.0161262,0.035097),(0.589241,8.90156e-07))
9 (D20A_12:78.0334,(((D15A_18:42.0569,(D19A_7:24.509,D1A_16:24.509)_12:17.5479)_12:4.15507,(D8A_15:16.7282,(D5A_9:8.752,(D23A_4:7.71805,(D14A_16:4.17075,D13A_18:4.17075)_16:3.5473)_11:1.03395)_11:7.97622)_12:29.4837)_12:26.7067,(D17A_6:63.6391,(D10A_7:24.4991,((D2A_18:5.87362,D4A_8:5.87362)_10:15.5526,(D3A_12:14.2972,((D18A_7:5.4519,D16A_7:5.4519)_7:4.97616,(D7A_12:8.67218,(D9A_9:7.36182,(D29A_5:5.72085,D24A_3:5.72085)_5:1.64097)_8:1.31036)_8:1.75588)_8:3.86919)_9:7.12897)_9:3.07286)_9:39.14)_10:9.2796)_11:5.11474)_11 0 ((0.598705,0.645638),(0.00365378,0.809369),(0.0009555,0.0125544),(0.631209,0.862035),(0.0260629,0.305784),(0.0180608,0.535927),(7.04062e-10,1.90775e-07),(0.662806,0.0261159),(0.360005,0.340888),(0.0448611,0.634028),(0.154706,0.581483),(1.0845e-10,0.00625356),(0.205553,0.660985),(0.00987448,0.123706),(0.601659,0.601659),(0.143385,0.526528),(9.41931e-05,0.526528),(0.0928989,1.15805e-06),(0.576188,0.00149766))
10 (D20A_5:78.0334,(((D15A_2:42.0569,(D19A_1:24.509,D1A_8:24.509)_6:17.5479)_6:4.15507,(D8A_7:16.7282,(D5A_6:8.752,(D23A_5:7.71805,(D14A_5:4.17075,D13A_6:4.17075)_6:3.5473)_6:1.03395)_6:7.97622)_6:29.4837)_6:26.7067,(D17A_16:63.6391,(D10A_9:24.4991,((D2A_21:5.87362,D4A_14:5.87362)_15:15.5526,(D3A_24:14.2972,((D18A_15:5.4519,D16A_6:5.4519)_12:4.97616,(D7A_11:8.67218,(D9A_6:7.36182,(D29A_11:5.72085,D24A_20:5.72085)_12:1.64097)_12:1.31036)_12:1.75588)_12:3.86919)_13:7.12897)_13:3.07286)_12:39.14)_10:9.2796)_8:5.11474)_8 0 ((0.179734,0.613475),(0.00360542,0.721388),(1.24342e-05,0.0913331),(0.573495,0.790707),(0.151515,0.61805),(0.631228,0.5201),(0.17999,0.55677),(0.111272,0.573495),(0.147873,0.031425),(0.00786196,0.169418),(0.029978,0.0610304),(4.00934e-07,0.282793),(0.0691518,0.706397),(9.69715e-10,0.169874),(0.00150494,1.83028e-08),(0.631209,0.538996),(0.33435,0.538996),(1.41393e-07,0.538996),(0.239667,4.62591e-10))
11 (D20A_4:78.0334,(((D15A_0:42.0569,(D19A_5:24.509,D1A_3:24.509)_4:17.5479)_4:4.15507,(D8A_3:16.7282,(D5A_6:8.752,(D23A_8:7.71805,(D14A_12:4.17075,D13A_7:4.17075)_7:3.5473)_7:1.03395)_6:7.97622)_4:29.4837)_4:26.7067,(D17A_5:63.6391,(D10A_4:24.4991,((D2A_6:5.87362,D4A_3:5.87362)_6:15.5526,(D3A_16:14.2972,((D18A_22:5.4519,D16A_19:5.4519)_19:4.97616,(D7A_18:8.67218,(D9A_22:7.36182,(D29A_3:5.72085,D24A_9:5.72085)_9:1.64097)_16:1.31036)_16:1.75588)_16:3.86919)_15:7.12897)_7:3.07286)_6:39.14)_5:9.2796)_5:5.11474)_5 0 ((0.628407,0.576188),(0.000277421,0.670103),(0.149032,0.330282),(0.550967,0.738592),(0.24927,0.00562789),(0.631228,0.0103271),(0.0816348,0.565258),(1.04263e-07,0.584096),(0.398388,0.624745),(0.854415,0.269686),(0.0421178,0.0307219),(0.589241,5.42265e-05),(0.35246,1.16779e-10),(0.293169,0.0759091),(0.00509157,0.711965),(0.00181296,0.550964),(0.0781961,0.550964),(3.48735e-06,3.9836e-14),(9.90516e-10,0.624724))
12 (D20A_13:78.0334,(((D15A_17:42.0569,(D19A_6:24.509,D1A_7:24.509)_8:17.5479)_11:4.15507,(D8A_12:16.7282,(D5A_10:8.752,(D23A_13:7.71805,(D14A_7:4.17075,D13A_6:4.17075)_7:3.5473)_10:1.03395)_10:7.97622)_11:29.4837)_11:26.7067,(D17A_24:63.6391,(D10A_5:24.4991,((D2A_5:5.87362,D4A_14:5.87362)_6:15.5526,(D3A_2:14.2972,((D18A_0:5.4519,D16A_0:5.4519)_0:4.97616,(D7A_2:8.67218,(D9A_11:7.36182,(D29A_6:5.72085,D24A_4:5.72085)_5:1.64097)_5:1.31036)_3:1.75588)_3:3.86919)_3:7.12897)_5:3.07286)_5:39.14)_11:9.2796)_11:5.11474)_11 0 ((0.345268,0.645638),(0.00268311,0.0109791),(0.13445,0.489449),(0.622515,0.854719),(0.255529,0.287678),(0.689961,0.532826),(0.00224744,6.486e-05),(0.584096,0.12761),(0.844818,0.717375),(4.01828e-06,0.000412314),(0.74293,0.548019),(0.135429,3.82347e-12),(0.120557,0.00292153),(0.178783,0.529694),(0.5,0.5),(1.75285e-06,0.510206),(0.110811,7.05994e-05),(2.28054e-08,0.516836),(0.0423294,0.115291))
13 (D20A_0:78.0334,(((D15A_4:42.0569,(D19A_7:24.509,D1A_4:24.509)_6:17.5479)_6:4.15507,(D8A_13:16.7282,(D5A_12:8.752,(D23A_12:7.71805,(D14A_15:4.17075,D13A_14:4.17075)_14:3.5473)_12:1.03395)_12:7.97622)_12:29.4837)_6:26.7067,(D17A_6:63.6391,(D10A_9:24.4991,((D2A_9:5.87362,D4A_7:5.87362)_7:15.5526,(D3A_8:14.2972,((D18A_9:5.4519,D16A_7:5.4519)_7:4.97616,(D7A_7:8.67218,(D9A_8:7.36182,(D29A_6:5.72085,D24A_7:5.72085)_7:1.64097)_7:1.31036)_7:1.75588)_7:3.86919)_7:7.12897)_7:3.07286)_7:39.14)_6:9.2796)_6:5.11474)_6 0 ((0.000100917,0.589241),(0.181972,0.721388),(0.214288,0.0421178),(0.573495,9.12573e-05),(0.273483,0.696127),(0.713348,0.538996),(0.696127,0.00941183),(0.093561,0.647616),(0.777025,0.64366),(0.869192,0.310088),(0.113193,0.565258),(0.00879369,0.601659),(0.725164,0.633344),(0.155006,0.565258),(0.00879369,0.601659),(0.584096,0.523331),(0.647637,0.523331),(0.0816348,0.523331),(0.154708,0.601659))
14 (D20A_3:78.0334,(((D15A_8:42.0569,(D19A_7:24.509,D1A_6:24.509)_7:17.5479)_7:4.15507,(D8A_5:16.7282,(D5A_11:8.752,(D23A_6:7.71805,(D14A_12:4.17075,D13A_10:4.17075)_10:3.5473)_9:1.03395)_9:7.97622)_7:29.4837)_7:26.7067,(D17A_6:63.6391,(D10A_6:24.4991,((D2A_3:5.87362,D4A_3:5.87362)_3:15.5526,(D3A_10:14.2972,((D18A_6:5.4519,D16A_6:5.4519)_6:4.97616,(D7A_14:8.67218,(D9A_8:7.36182,(D29A_14:5.72085,D24A_12:5.72085)_12:1.64097)_11:1.31036)_11:1.75588)_9:3.86919)_9:7.12897)_6:3.07286)_6:39.14)_6:9.2796)_6:5.11474)_6 0 ((0.124308,0.589241),(0.362634,0.741688),(0.786269,0.458634),(0.584096,0.809019),(0.0273977,0.0161262),(0.0315194,0.529693),(0.000556168,0.0459542),(0.0113452,0.613472),(0.228632,0.64366),(0.869192,0.824997),(0.766746,0.55677),(0.548022,0.548022),(0.00141672,0.000541599),(0.193972,0.581483),(0.589241,0.589241),(0.000108085,0.000667175),(0.00409853,0.535927),(0.00102403,0.0189206),(0.0232894,0.65536))
代码：
#!/public/home/wangwen_lab/zhangjiexiong/anaconda3/bin/python
import re,sys
class Node:
def __init__(self,nodeNum,geneNum,nodeLength,upbranch,downbranch,s):
self.nodeNum = nodeNum
self.geneNum = geneNum
self.upbranch = upbranch
self.downbranch = downbranch
self.nodeLength = nodeLength
self.nstring = s
class family:
def __init__(self,me,brother,father,uncle="NULL",ancestor="NULL"):
self.me = me
self.brother = brother
self.father = father
self.uncle = uncle
self.ancestor = ancestor
def findComma(s): # find the core comma of a tree string
place,sta = 0,0
for i in s:
if i == "(":
sta += 1
elif i == ")":
sta -= 1
if i == ",":
if sta == 1:
commaplace = place
break
place += 1
return commaplace
def findPairedBracket(s): #find the coord of fist "(" and the last ")"
place,sta = 0,0
for i in s:
if i == "(":
sta += 1
if sta == 1:
firstbracket = place
elif i == ")":
sta -= 1
if place != 0 and sta == 0:
pairedbracket = place
place += 1
return [firstbracket,pairedbracket]
def NodeInfo(s): #store the information of the node to the class--Node which is definded in the first
treelen = len(s)
if "(" in s:
bracket = findPairedBracket(s)
nodeInfo = s[bracket[1]+1:treelen]
try:
nodeNum = nodeInfo.split(">")[0].split("<")[1]
except:
print("Error"+s)
geneNum = nodeInfo.split("_")[1].split(":")[0]
nodeLength = nodeInfo.split(":")[1]
nodeContent = s[0:bracket[1]+1]
commaplace = findComma(nodeContent)
nodelength = len(nodeContent)
upbranch = nodeContent[1:commaplace]
downbranch = nodeContent[commaplace+1:nodelength-1]
node = Node(nodeNum,geneNum,nodeLength,upbranch,downbranch,s)
else: #D20A_82:78.0334
geneNum = s.split("_")[1].split(":")[0]
nodeNum = s.split(">")[0].split("<")[1]
nodeLength = s.split(":")[1]
node = Node(nodeNum,geneNum,nodeLength,"","",s)
return node
def judgeNode(s): #judge whether the string is a tree
if type(s) == type('str'):
if "(" in s:
bracket = findPairedBracket(s)
tail = s[bracket[1]::]
if re.match("\)<\d+>_\d+",tail):
return 1
else:
return 0
else:
return 1
def circle(node): # !!!! the most important function which carry out the iteration of the tree to send each subtrees to a global list named "dicNode"
if node != "":
node = NodeInfo(node)
if judgeNode(node):
dicNode.append(node)
circle(node.upbranch)
circle(node.downbranch)
else:
dicNode.append(node)
def judgeCertainSpecies(node,species): #judge whether the input branch "species" is the only branch under the node's two subbranch and distinguish whether the train is in upbranch or downbranch
if species in node.upbranch:
branch = node.upbranch
elipbranch = branch.replace(species,"")
if "(" in elipbranch:
return 0
else:
return "up"
elif species in node.downbranch:
branch = node.downbranch
elipbranch = branch.replace(species,"")
if "(" in elipbranch:
return 0
else:
return "down"
else:
return 0
def findDirectFamiliesOfAimedNode(node): #node is a string type. This function can find the adjioning branch of the target node and return the adjioning nodes
for i in dicNode:
if i.upbranch != "":
if judgeCertainSpecies(i,node) != 0:
father = "("+i.upbranch+","+i.downbranch+")"+"<"+i.nodeNum+">"+"_"+i.geneNum+":"+i.nodeLength
if judgeCertainSpecies(i,node) == "up":
me = i.upbranch
brother = i.downbranch
elif judgeCertainSpecies(i,node) =="down":
brother = i.upbranch
me = i.downbranch
try:
families = family(me,brother,father)
except:
print("Error"+node)
return families
dicNode = []
#def judgeGFtyoe(tree,target):
def getTragetGeneNum(tree,target):
tree = tree+":0"
circle(tree)
for i in dicNode:
ptree = i.nstring
a = re.sub("_[^_]*$","",ptree)
if a[-3::] == target or a[-4::]== target:
target = a.replace(target,"")
allfolks = findDirectFamiliesOfAimedNode(target)
myInfoNum = allfolks.me.split("_")[-1].split(":")[0]
return int(myInfoNum)
def addnodes(tree1,treenode): #see addNode.py
strains = re.findall("\)_",tree1)
nodes = re.findall("\)<\d+>",treenode)
for i in nodes:
tree1 = tree1.replace(")_",i+"_",1)
nodes = re.findall(r"A<\d+>",treenode)
for i in nodes:
tree1 = tree1.replace("A_",i+"_",1)
return tree1
f = open(sys.argv[1],"r")
flag = 0
treelist = []
tplist = []
nplist = []
trenumlist = []
for i in f:
if flag == 0:
if re.match("'ID'",i):
flag = 1
continue
elif re.match("# IDs of nodes:",i):
treenode = i.strip().split(":")[1]
elif re.match("# Output format for:",i):
idstring = i.strip().split(":")[2].strip(" ")
idstring = idstring.replace(")","")
idstring = idstring.replace("(","")
idstring = idstring.replace(" ",",")
idlist = idstring.split(",")
else:
wholeLine = i.strip().split()
trenumlist.append(wholeLine[0])
treelist.append(wholeLine[1])
tplist.append(wholeLine[2])
nplist.append(wholeLine[3])
def cleanbrac(s):
s = s.replace(")","")
s = s.replace("(","")
sl = s.split(",")
return sl
target = ["<7>","<19>"]
Excount = 0
Cocount = 0
Nccount = 0
count = 0
explist = []
conlist = []
nchlist = []
pvalue = 0.5
for i in range(len(treelist)):
if float(tplist[i]) > 0.01:
continue
tree = treelist[i]
tree = addnodes(tree,treenode)
dicNode = []
tagret1GnenNum = getTragetGeneNum(tree,target[0])
dicNode = []
target2GnenNum = getTragetGeneNum(tree,target[1])
tp = float(tplist[i])
np = nplist[i]
npl = cleanbrac(np)
c = zip(idlist,npl)
tnum1 = target[0].split(">")[0].split("<")[1]
tnum2 = target[1].split(">")[0].split("<")[1]
for j in c:
if tnum1 == j[0]:
nodep1 = j[1]
elif tnum2 == j[0]:
nodep2 = j[1]
if nodep1 == "-" or nodep2 == "-":
count += 1
continue
else:
nodep1 = float(nodep1)
nodep2 = float(nodep2)
# print(count)
if nodep1<= pvalue and nodep2 <= pvalue:
# print(trenumlist[i])
# else:
# print(nodep1,trenumlist[i])
if tagret1GnenNum < target2GnenNum:
# print(tnum1,tnum2)
CEtype = "Expansion"
Excount += 1
explist.append(trenumlist[i])
elif tagret1GnenNum == target2GnenNum:
CEtype = "NoChange"
Nccount += 1
nchlist.append(trenumlist[i])
# print(tagret1GnenNum,target2GnenNum,trenumlist[i])
else:
CEtype = "Contraction"
Cocount += 1
conlist.append(trenumlist[i])
#print(tagret1GnenNum,target2GnenNum,trenumlist[i])
count += 1
print("{}_vs_{}:\tExpansion:{}\tContraction:{}\tNoChange:{}".format(target[0],target[1],Excount,Cocount,Nccount))
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