Question

我需要从前列腺切除术最终诊断报告的平面文件中提取格里森分数。这些分数总是有格里森这个词和两个加起来的数字。二十多年来，人类对这些进行了打字。包括空白和修饰符的各种约定。下面是我目前为止的Backus-Naur表格和两个示例记录。仅仅针对前列腺切除术，我们正在查看超过一千个病例。

我正在使用pyparsing因为我正在学习python，并且对我对正则表达式编写的非常有限的记忆没有美好的回忆。

我的问题：我如何在不解析这些最终诊断中可能会或可能不会出现的其他可选数据的情况下，将这些Gleason分数剔除？

num = Word(nums)
record ::= accessionDate + accessionNumber + patMedicalRecordNum + finalDxText
accessionDate ::= num + "/" + num + "/" num
accessionNumber ::= "S" + num + "-" + num
patMedicalRecordNum ::= num + "/" + num + "-" + num + "-" + num
finalDxText ::= listOfParts + optionalComment + optionalpTNMStage
listOfParts ::= OneOrMore(part)
part ::= <multiline idiosyncratic freetext which may contain a Gleason score I want> + optionalpTNMStage
optionalComment ::= <multiline idiosyncratic freetext which may contain a Gleason score I don't want>
optionalpTNMStage ::= <multiline idiosyncratic freetext which may contain a Gleason score I don't want>


01/01/11  S11-55555 20/444-55-6666 A.  PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:                           
                                   -  ADENOCARCINOMA.                                                      

                                   TOTAL GLEASON SCORE:  GLEASON 5+4=9                                     
                                   TUMOR LOCATION:  BILATERAL                                              
                                   TUMOR QUANTITATION:  15% OF PROSTATE INVOLVED BY TUMOR                  
                                   EXTRAPROSTATIC EXTENSION:  PRESENT AT RIGHT POSTERIOR                   
                                   SEMINAL VESICLE INVASION:  PRESENT                                      
                                   MARGINS:  UNINVOLVED                                                    
                                   LYMPHOVASCULAR INVASION:  PRESENT                                       
                                   PERINEURAL INVASION:  PRESENT                                           
                                   LYMPH NODES (SPECIMENS B AND C):                                        
                                      NUMBER EXAMINED:  25                                                 
                                      NUMBER INVOLVED:  1                                                  
                                      DIAMETER OF LARGEST METASTASIS:  1.7 mm                              
                                   ADDITIONAL FINDINGS:  HIGH-GRADE PROSTATIC INTRAEPITHELIAL NEOPLASIA,   
                                      ACUTE AND CHRONIC INFLAMMATION, INTRADUCTAL EXTENSION OF INVASIVE    
                                      CARCINOMA                                                            

                                   PATHOLOGIC STAGE:  pT3b N1 MX                                           

                               B.  LYMPH NODES, RIGHT PELVIC, EXCISION:                                    
                                   -  ONE OF SEVENTEEN LYMPH NODES POSITIVE FOR METASTASIS (1/17).         

                               C.  LYMPH NODES, LEFT PELVIC, EXCISION:                                     
                                   -  EIGHT LYMPH NODES NEGATIVE FOR METASTASIS (0/8).                     
01/02/11  S11-4444 20/111-22-3333 PROSTATE AND SEMINAL VESICLES, PROSTATECTOMY:                               
                                  - ADENOCARCINOMA.                                                        
                                    GLEASON SCORE:  3 + 3 = 6 WITH TERTIARY PATTERN OF 5.                                             
                                    TUMOR QUANTITATION:  APPROXIMATELY 10% BY VOLUME.                      
                                    TUMOR LOCATION:  BILATERAL.                                            
                                    EXTRAPROSTATIC EXTENSION:  NOT IDENTIFIED.                             
                                    MARGINS:  NEGATIVE.                                                    
                                    PERINEURAL INVASION:  IDENTIFIED.                                      
                                    LYMPH-VASCULAR INVASION:  NOT IDENTIFIED.                              
                                    SEMINAL VESICLE/VASA DEFERENTIA INVASION: NOT IDENTIFIED.              
                                    LYMPH NODES:  NONE SUBMITTED.                                          
                                    OTHER:  HIGH GRADE PROSTATIC INTRAEPITHELIAL NEOPLASIA.                
                               PATHOLOGIC STAGE (pTNM):  pT2c NX.

完全披露：我是一名做研究的医生;这是我第一次使用python进行实际操作。我已经阅读了Lutz的学习Python，Shaw的艰难学习Python，并完成了各种问题集。我已经在这个论坛上审阅了许多与pyparsing相关的问题，pyparsing wiki，我买了并阅读了McGuire先生的Pyparsing入门。也许我问一个问题，当我真的应该被告知我站在“当你必须编写解析器时，沮丧的死亡螺旋很常见”（McGuire，17）？我不知道。到目前为止，我很高兴能够开展真正的项目。

Answer 1

看一下pyparsing中的SkipTo解析元素。如果为num + num = num部分定义一个pyparsing结构，你应该可以使用SkipTo跳过“Gleason”和那之间的任何内容。大致相同（未经测试的pseuo-pyparsing）：

score = num + "+" + num + "=" num
Gleason = "Gleason" + SkipTo(score) + score

默认情况下，PyParsing会跳过空格，而使用SkipTo，你可以跳过任何与你想要的格式不符的内容。

Answer 2

以下是抽取患者数据和任何匹配的格里森数据的示例。

from pyparsing import *
num = Word(nums)
accessionDate = Combine(num + "/" + num + "/" + num)("accDate")
accessionNumber = Combine("S" + num + "-" + num)("accNum")
patMedicalRecordNum = Combine(num + "/" + num + "-" + num + "-" + num)("patientNum")
gleason = Group("GLEASON" + Optional("SCORE:") + num("left") + "+" + num("right") + "=" + num("total"))
assert 'GLEASON 5+4=9' == gleason
assert 'GLEASON SCORE:  3 + 3 = 6' == gleason

patientData = Group(accessionDate + accessionNumber + patMedicalRecordNum)
assert '01/02/11  S11-4444 20/111-22-3333' == patientData

partMatch = patientData("patientData") | gleason("gleason")

lastPatientData = None
for match in partMatch.searchString(data):
    if match.patientData:
        lastPatientData = match
    elif match.gleason:
        if lastPatientData is None:
            print "bad!"
            continue
        print "{0.accDate}: {0.accNum} {0.patientNum} Gleason({1.left}+{1.right}={1.total})".format(
                        lastPatientData.patientData, match.gleason
                        )

打印：

01/01/11: S11-55555 20/444-55-6666 Gleason(5+4=9)
01/02/11: S11-4444 20/111-22-3333 Gleason(3+3=6)

Answer 3

gleason = re.compile("gleason\d+\d=\d")
scores = set()
for record in records:
    for line in record.lower().split("\n"):
        if "gleason" in line:
            scores.add(gleason.match(line.replace(" ", "")).group(0)[7:])

或者其他什么

Pyparsing：提取可变长度，可变内容，变量空白子字符串

3 个答案: