将XML文件转换为Python中的列表列表

编程问答 2022-08-14

问题描述

我有一个来自HMDB和Saliva Metabolites数据的数据集。

此数据是XML文件。我想做的就是用Python将这个XML文件转换为列表列表（嵌套列表），但是，我不希望列表中的所有节点。

已编辑：这是一种代谢物的部分数据的示例 

<?xml version="1.0" encoding="UTF-8"?>
<hmdb xmlns="http://www.hmdb.ca">
<Metabolite>
  <version>4.0</version>
  <creation_date>2005-11-16 15:48:42 UTC</creation_date>
  <update_date>2019-01-11 19:13:56 UTC</update_date>
  <accession>HMDB0000001</accession>
  <status>quantified</status>
  <secondary_accessions>
    <accession>HMDB00001</accession>
    <accession>HMDB0004935</accession>
    <accession>HMDB0006703</accession>
    <accession>HMDB0006704</accession>
    <accession>HMDB04935</accession>
    <accession>HMDB06703</accession>
    <accession>HMDB06704</accession>
  </secondary_accessions>
  <name>1-Methylhistidine</name>
  <cs_description>1-Methylhistidine,also kNown as 1-mhis,belongs to the class of organic compounds kNown as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carBoxy group,or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine has been found in human muscle and skeletal muscle tissues,and has also been detected in most biofluids,including cerebrospinal fluid,saliva,blood,and feces. Within the cell,1-methylhistidine is primarily located in the cytoplasm. 1-Methylhistidine participates in a number of enzymatic reactions. In particular,1-Methylhistidine and Beta-alanine can be converted into anserine; which is catalyzed by the enzyme carnosine synthase 1. In addition,Beta-Alanine and 1-methylhistidine can be biosynthesized from anserine; which is mediated by the enzyme cytosolic non-specific dipeptidase. In humans,1-methylhistidine is involved in the histidine Metabolism pathway. 1-Methylhistidine is also involved in the Metabolic disorder called the histidinemia pathway.</cs_description>
  <description>One-methylhistidine (1-MHis) is derived mainly from the anserine of dietary flesh sources,especially poultry. The enzyme,carnosinase,splits anserine into b-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely,genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat,especially red meat.</description>
  <synonyms>
    <synonym>(2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoic acid</synonym>
    <synonym>1-Methylhistidine</synonym>
    <synonym>Pi-methylhistidine</synonym>
    <synonym>(2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoate</synonym>
    <synonym>1 Methylhistidine</synonym>
    <synonym>1-Methyl histidine</synonym>
  </synonyms>
  <chemical_formula>C7H11N3O2</chemical_formula>
  <smiles>CN1C=NC(C[C@H](N)C(O)=O)=C1</smiles>
  <inchikey>BRMWTNUJHUMWMS-LURJTMIESA-N</inchikey>
<diseases>
    <disease>
      <name>Kidney disease</name>
      <omim_id/>
      <references>
        <reference>
          <reference_text>McGregor DO,Dellow WJ,Lever M,George PM,Robson RA,ChAmbers ST: Dimethylglycine accumulates in uremia and predicts elevated plasma homocysteine concentrations. Kidney Int. 2001 Jun;59(6):2267-72.</reference_text>
          <pubmed_id>11380830</pubmed_id>
        </reference>
        <reference>
          <reference_text>Ehrenpreis ED,Salvino M,Craig RM: Improving the serum D-xylose test for the identification of patients with small intestinal malabsorption. J Clin Gastroenterol. 2001 Jul;33(1):36-40.</reference_text>
          <pubmed_id>11418788</pubmed_id>
        </reference>
        <reference>
         </reference>
      </references>
    </disease>
    <disease>

导入文件：

import xml.etree.ElementTree as et

data1 = et.parse('D:/path/to/Tal/my/HMDB/DataSets/saliva_Metabolites/saliva_Metabolites.xml')
root = data1.getroot()

现在，不确定如何选择特定节点。意思是，我的目标是创建一个代谢物列表，列表中的每个代谢物都将包含一个节点列表（例如<accession>，<name>，<synonyms>和<diseases_name>）

依次，这些元素将包含另一个列表（例如，在<synonyms>内将有一个值名称列表，或者在<diseases_name>内将是疾病名称列表，每种疾病都将包含pub_id值的列表）。

# To access the 4'th node of the first Metabolit

>>  root[0][3].text
'HMDB0000001'

其中root[0][3]代表<accession>节点。

试图通过打印来运行循环，所以我会理解循环的输出，但收到None的列表

for node in root:
    print(node.find('accession'))
None
None
None
None
None
.
.
.

也尝试过

>> root.findall('./Metabolite/accession')
[]

但收到空括号

获取我尝试过的第一个代谢产物的同义词列表：

>> root[0][9].text
'\n    '

# This gave the first value of synonyms
root[0][9][0].text
'\n    '

我用这些问题来找到答案：

  1. How do I parse XML in Python?
  2. how to create a list of elements from an XML file in python
  3. Python: XML file to pandas dataframe
  4. Convert XML into Lists of Tags and Values with Python
  5. Generating nested lists from XML doc

任何提示，想法都会有所帮助，谢谢您的宝贵时间

解决方法

您将忽略XML中的名称空间。

<hmdb xmlns="http://www.hmdb.ca">

表示没有<hmdb>元素。 <hmdb>名称空间中有一个http://www.hmdb.ca 。并且由于这是该元素的默认名称空间，因此所有后代元素都位于同一名称空间中，除非它们将其覆盖。

所以这个

root.findall('./metabolite/accession')

将不会返回任何内容，因为您在错误的名称空间中搜索。

为方便起见，让我们在http://www.hmdb.ca命名空间中进行句柄h的搜索：

ns = {
    "h": "http://www.hmdb.ca"
}

accession = root.findall('./h:metabolite/h:accession',ns)
print(accession)

这将找到一个元素（请参见在打印时如何明确表示名称空间）：

[<Element '{http://www.hmdb.ca}accession' at 0x03E6E7B0>]

您可以在ElementTree中使用相同的显式语法，但是很快就会变得笨拙：

t.findall('./{http://www.hmdb.ca}metabolite/{http://www.hmdb.ca}accession')

使用prefix:较短（标准）的语法可以更好地工作。

elementtreelistpythonxmlxmlxmlxmlxmlxml