Question

With the help from several people here at Stackoverflow I came up with the following code:

import lxml.etree

f = open("PaVE.tre.xml", "r")
out = open("PaVE.2.xml", "a")
data = f.read()
line=["HPV16","Alpha"]

tree = lxml.etree.XML(data)
nsmap = {'phylo': 'http://www.phyloxml.org'}
matches = tree.xpath('//phylo:name[text()="HPV16"]', namespaces=nsmap)

for e in matches:
    #do something fun

However, I am hard-coding the HPV16 into the xpath expression. I would like to take the HPV16 from line[0]. I was thinking something like:

matches = tree.xpath('//phylo:name[text()='+line[0]+']', namespaces=nsmap)

However, that does not seem to work!
As always, any help would be appreciated

EDIT:
I added a couple of lines from the xml file as was requested:

<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.phyloxml.org" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd">
<phylogeny rooted="true">
  <clade>
    <clade>
      <branch_length>0.5</branch_length>
      <clade>
        <name>HPV16</name>
        <branch_length>1.0</branch_length>
      </clade>
      <clade>

Answer 1

You forgot the quotes in your XPath expression:

>>> '//phylo:name[text()='+line[0]+']'
'//phylo:name[text()=something]'

I would do this instead:

>>> '//phylo:name[text()="%s"]' % line[0]
'//phylo:name[text()="something"]'