shell或者python脚本提取xml文件中信息

Question

有一个xml文本test.xml，里面的主要信息内容是Hit，提取Hit信息中的两个tag内容，组成新的结果res.txt。希望脚本运行是这样的：bash xml-info.sh test.xml，或者python xml-info.py test.xml，自动生成res.txt结果。

hit信息基本组成单位，要想利用shell脚本或者python脚本提取xml文件里面的两个信息，Hit_accession和Hsp_hseq：

<Hit>
  <Hit_num>1</Hit_num>
  <Hit_id>gnl|SRA|SRR6675308.2504034.2</Hit_id>
  <Hit_def>2504034</Hit_def>
  <Hit_accession>SRR6675308.2504034.2</Hit_accession>
      <Hsp_align-len>50</Hsp_align-len>
      <Hsp_qseq>GFRKLPMGVGLSPFLLAQFTSSLASMVRRNFPHCMVFAYMDDVVLGAKSV</Hsp_qseq>
      <Hsp_hseq>GFRKIPMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKSV</Hsp_hseq>
      <Hsp_midline>GFRK+PMGVGLSPFLLAQFTS++ S+VRR FPHC+ F+YMDDVVLGAKSV</Hsp_midline>
    </Hsp>
  </Hit_hsps>
</Hit>

输出成为res.txt，格式如下，第一行Hit_accession，以>开头（不知道为啥帖子里面显示不出来，用“>”代替），第二行Hsp_hseq，直接是Hsp_hseq内容
“>”SRR6675308.2504034.2
GFRKIPMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKSV

测试文件test.xml

<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
    </Parameters>
  </BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
  <Iteration_iter-num>1</Iteration_iter-num>
  <Iteration_query-len>838</Iteration_query-len>
<Iteration_hits>
<Hit>
  <Hit_num>1</Hit_num>
  <Hit_id>gnl|SRA|SRR6675308.2504034.2</Hit_id>
  <Hit_def>2504034</Hit_def>
  <Hit_accession>SRR6675308.2504034.2</Hit_accession>
  <Hit_len>150</Hit_len>
  <Hit_hsps>
    <Hsp>
      <Hsp_gaps>0</Hsp_gaps>
      <Hsp_align-len>50</Hsp_align-len>
      <Hsp_qseq>GFRKLPMGVGLSPFLLAQFTSSLASMVRRNFPHCMVFAYMDDVVLGAKSV</Hsp_qseq>
      <Hsp_hseq>GFRKIPMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKSV</Hsp_hseq>
      <Hsp_midline>GFRK+PMGVGLSPFLLAQFTS++ S+VRR FPHC+ F+YMDDVVLGAKSV</Hsp_midline>
    </Hsp>
  </Hit_hsps>
</Hit>
<Hit>
  <Hit_num>2</Hit_num>
  <Hit_id>gnl|SRA|SRR10821940.27046739.1</Hit_id>
  <Hit_def>27046739</Hit_def>
  <Hit_accession>SRR10821940.27046739.1</Hit_accession>
  <Hit_len>150</Hit_len>
  <Hit_hsps>
    <Hsp>
      <Hsp_num>1</Hsp_num>
      <Hsp_gaps>0</Hsp_gaps>
      <Hsp_align-len>50</Hsp_align-len>
      <Hsp_qseq>GFRKLPMGVGLSPFLLAQFTSSLASMVRRNFPHCMVFAYMDDVVLGAKSV</Hsp_qseq>
      <Hsp_hseq>GFRKIPMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKSV</Hsp_hseq>
      <Hsp_midline>GFRK+PMGVGLSPFLLAQFTS++ S+VRR FPHC+ F+YMDDVVLGAKSV</Hsp_midline>
    </Hsp>
  </Hit_hsps>
</Hit>
<Hit>
  <Hit_num>3</Hit_num>
  <Hit_id>gnl|SRA|SRR10821940.8209197.2</Hit_id>
  <Hit_def>8209197</Hit_def>
  <Hit_accession>SRR10821940.8209197.2</Hit_accession>
  <Hit_len>150</Hit_len>
  <Hit_hsps>
    <Hsp>
      <Hsp_query-frame>0</Hsp_query-frame>
      <Hsp_hit-frame>-1</Hsp_hit-frame>
      <Hsp_gaps>0</Hsp_gaps>
      <Hsp_align-len>50</Hsp_align-len>
      <Hsp_qseq>GFRKLPMGVGLSPFLLAQFTSSLASMVRRNFPHCMVFAYMDDVVLGAKSV</Hsp_qseq>
      <Hsp_hseq>GFRKIPMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKSV</Hsp_hseq>
      <Hsp_midline>GFRK+PMGVGLSPFLLAQFTS++ S+VRR FPHC+ F+YMDDVVLGAKSV</Hsp_midline>
    </Hsp>
  </Hit_hsps>
</Hit>
</Iteration_hits>
  <Iteration_stat>
    <Statistics>
      <Statistics_db-num>1266261802</Statistics_db-num>
      <Statistics_db-len>1968308817</Statistics_db-len>
    </Statistics>
  </Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>

Answer 1

将test.xml文件放在xml-info.py的同一目录下，运行如下代码即可：

import argparse
from lxml import etree
parser=argparse.ArgumentParser()
parser.add_argument('f',default='test.xml')
parser.add_argument('-o', default='res.txt')
args=parser.parse_args()
fname=args.f
with open(fname,'r') as fn:
    dt=fn.read()
html=etree.XML(dt)
a=html.xpath('//Hit_accession/text()')
b = html.xpath('//Hsp_hseq/text()')
s='\n'.join(['>'+x+'\n'+y for x,y in zip(a,b)])
with open(args.o,'w',encoding='utf-8') as fw:
    fw.write(s)

运行结果的res.txt中内容：

>SRR6675308.2504034.2
GFRKIPMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKSV
>SRR10821940.27046739.1
GFRKIPMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKSV
>SRR10821940.8209197.2
GFRKIPMGVGLSPFLLAQFTSAICSVVRRAFPHCLAFSYMDDVVLGAKSV

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