DrugBank XML解析

想当初我还曾经用爬虫爬过drugbank的信息，现在想想真的是傻

<?xml version="1.0" encoding="UTF-8"?>
<drugbank xmlns="http://www.drugbank.ca" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.drugbank.ca http://www.drugbank.ca/docs/drugbank.xsd" version="5.1" exported-on="2020-01-03">
<drug type="biotech" created="2005-06-13" updated="2020-01-02">
  <drugbank-id primary="true">DB00001</drugbank-id>
  <drugbank-id>BTD00024</drugbank-id>
  <drugbank-id>BIOD00024</drugbank-id>
  <name>Lepirudin</name>
  <description>Lepirudin is identical to natural hirudin except for substitution of leucine for isoleucine at the N-terminal end of the molecule and the absence of a sulfate group on the tyrosine at position 63. It is produced via yeast cells. Bayer ceased the production of lepirudin (Refludan) effective May 31, 2012.</description>

#对了我的版本是python3
#安装一个包
pip install lxml
#导入
import lxml
from lxml import etree
#打开xml，读取内容
f=open('full_database.xml','r')
xml_text=f.read()
#读取
xml_test=etree.fromstring(xml_text.encode('utf-8'))
#随便看下
xml_test
<Element {http://www.drugbank.ca}drugbank at 0x7f2fe62ff5f0>

type(xml_test)
lxml.etree._Element
#这样也可以
xml_test2=etree.parse('full_database.xml',etree.XMLParser())
#获得tree
root_tree = xml_test.getroottree()
#拿到根节点
troot = root.getroot()
#看下有多少个个节点，总共13475个药物
len(troot)
13475

#看下对于单个元素怎么操作
dir(troot)
['__bool__',
 '__class__',
 '__contains__',
 '__copy__',
 '__deepcopy__',
 '__delattr__',
 '__delitem__',
 '__dir__',
 '__doc__',
 '__eq__',
 '__format__',
 '__ge__',
 '__getattribute__',
 '__getitem__',
 '__gt__',
 '__hash__',
 '__init__',
 '__init_subclass__',
 '__iter__',
 '__le__',
 '__len__',
 '__lt__',
 '__ne__',
 '__new__',
 '__reduce__',
 '__reduce_ex__',
 '__repr__',
 '__reversed__',
 '__setattr__',
 '__setitem__',
 '__sizeof__',
 '__str__',
 '__subclasshook__',
 '_init',
 'addnext',
 'addprevious',
 'append',
 'attrib',
 'base',
 'clear',
 'cssselect',
 'extend',
 'find',
 'findall',
 'findtext',
 'get',
 'getchildren',
 'getiterator',
 'getnext',
 'getparent',
 'getprevious',
 'getroottree',
 'index',
 'insert',
 'items',
 'iter',
 'iterancestors',
 'iterchildren',
 'iterdescendants',
 'iterfind',
 'itersiblings',
 'itertext',
 'keys',
 'makeelement',
 'nsmap',
 'prefix',
 'remove',
 'replace',
 'set',
 'sourceline',
 'tag',
 'tail',
 'text',
 'values',
 'xpath']


#看下每个元素的长度
for i in troot:
    print(len(i))
#很明显，长短不一
50
50
49
48
50
52
49
50
50
50
48
#对第一个元素，也就是第一个药物打印相关标签以及文本内容
for i in troot[1]:
    print(i.tag)
    print(i.text)

#结果，好长，这里只放一部分
{http://www.drugbank.ca}drugbank-id
DB00002
{http://www.drugbank.ca}drugbank-id
BTD00071
{http://www.drugbank.ca}drugbank-id
BIOD00071
{http://www.drugbank.ca}name
Cetuximab
{http://www.drugbank.ca}description
Cetuximab is an epidermal growth factor receptor binding FAB. Cetuximab is composed of the Fv (variable; antigen-binding) regions of the 225 murine EGFr monoclonal antibody specific for the N-terminal portion of human EGFr with human IgG1 heavy and kappa light chain constant (framework) regions. Cetuximab is marketed under the brand Erbitux® by Eli Lilly and Company. In the United States, a regimen of cetuximab costs approximately $30,790 for an eight-week course.
#好了就这样