我正在寻找与 Python 中的 XML 相关的问题的解决方案。尽管 spectrum 不是根元素，但让我们假设它是针对此示例的。
<spectrum index="2" id="controller=0 scan=3" defaultArrayLength="485">
<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
<cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
<cvParam cvRef="MS" accession="MS:1000127" name="centroid mass spectrum" value=""/>
<precursorList count="1">
<precursor spectrumRef="controller=0 scan=2">
<isolationWindow>
<cvParam cvRef="MS" accession="MS:1000040" name="m/z" value="810.78999999999996"/>
<cvParam cvRef="MS" accession="MS:1000023" name="isolation width" value="2"/>
</isolationWindow>
<selectedIonList count="1">
<selectedIon>
<cvParam cvRef="MS" accession="MS:1000040" name="m/z" value="810.78999999999996"/>
</selectedIon>
</selectedIonList>
<activation>
<cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" value=""/>
<cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="35"/>
</activation>
</precursor>
</precursorList>
<binaryDataArrayList count="2">
<binaryDataArray encodedLength="5176">
<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
<binary>AAAAYHHsbEAAAADg3yptQAAAAECt7G1AAAAAAN8JbkAAAAAA.......hLJ==</binary>
</binaryDataArray>
<binaryDataArray encodedLength="2588">
<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value=""/>
<binary>ZFzUQWmVo0FH/o9BRfUyQg+xjUOzkZdC5k66QWk6HUSpqyZCsV1NQ......uH=</binary>
</binaryDataArray>
</binaryDataArrayList>
</spectrum>
我想要实现的是在树中找到所有 selectedIon 元素并回溯它的父元素谱。如果找到 selectedIon 元素，则
SelectedIon information:
Mass: 810.78999999999996
Spectra Info: ------------- index=2 id=controller=0 scan=3 length=485 General Info ------------ ms level=2 Msn spectrum= - centriod mass spectrum=- ..................... And all the cvParam name and value as above. Binary ------ m/z array = AAAAYHHsbEAAAADg3yptQAAAAECt7G1AAAA.....== intensity array = ZFzUQWmVo0FH/o9BRfUyQg+xjUOzkZdC5k66Q....5C77=
到目前为止我尝试了什么:
import xml.etree.ElementTree as ET
tree=ET.parse('file.mzml')
NS="{http://psi.hupo.org/ms/mzml}"
filesource=tree.findall('.//'+NS+'selectedIon') # Will get all selectedIon element from the tree
现在如何回溯到频谱元素/子元素以解析出上述相关信息？
我怎样才能成功？
请您参考如下方法:
XPath 将允许您访问祖先:“ancestor::spectrum”将返回 <spectrum>你所在的元素。如果使用 lxml，则可以使用完整的 XPath 语法来查找所需的元素。
from lxml import etree
tree = etree.XML('file.mzml')
NS = "{http://psi.hupo.org/ms/mzml}"
filesource = tree.findall('.//'+NS+'selectedIon')
spectrum = filesource.xpath('ancestor::spectrum')[0]
(我觉得，没测试过。。。)
更新:实际有效的代码:
from lxml import etree
tree = etree.parse('foo.xml')
for el in tree.findall(".//selectedIon"):
for top in el.xpath("ancestor::spectrum"):
print top
