blast结果下载

比对结果界面点击Download All，出现下拉菜单

分别下载XML及Hit Table(csv)

csv格式结果如下：

从左到右各列分别为：query id, subject id, identities, alignment length, mismatches, gap opens, qstart, qend, sstart, send, evalue, bit score, positives

csv数据缺少比对结果的注释

xml格式结果如下：

比对结果的描述为Hit_def标签

xml解析

  • parse方法：可接收文件名或打开的文件对象，生成ElementTree
  • getroot方法：获取根节点，生成Element。每个节点有tag, attrib, text, 节点可迭代，可通过索引获取子节点

整理blast比对结果

从xml文件中提取比对结果的注释，通过登录号与csv文件匹配合并，生成带有比对结果描述的文件

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from xml.etree import ElementTree
import pandas as pd


class ParseXML(object):
	def __init__(self, xmlpath):
		self.xmlpath = xmlpath

    # 获取xml根节点
	def getRoot(self):
		tree = ElementTree.parse(self.xmlpath)
		return tree.getroot()

    # 提取xml文件中的比对结果注释，同时提取对应的登录号用于匹配
	def getAnno(self, root):
		acc_list = []
		for elem in root[8].iter(tag='Hit_accession'):
			acc_list.append(elem.text + '.1')
		anno_list = []
		for elem in root[8].iter(tag='Hit_def'):
			anno_list.append(elem.text)
		return acc_list, anno_list

    # 生成结果文件并保存
	def getRes(self, outfile):
		root = self.getRoot()
		acc_list, anno_list = self.getAnno(root)
		res = pd.DataFrame({'subject id': acc_list, 'annotation': anno_list})
		res.to_csv(outfile, sep='\t', index=False)
		return res


class ParseCSV(object):
	def __init__(self, csvpath):
		self.csvpath = csvpath

    # 读取csv文件，添加表头
	def readCSV(self):
		df = pd.read_csv(self.csvpath, names=['query id', 'subject id', 'identities', 'alignment length', 'mismatches', 'gap opens', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bit score', 'positives'], header=0)
		return df

    # 根据登录号合并csv文件与xml提取的注释列
	def mergeRes(self, res, outfile):
		df = self.readCSV()
		merged = pd.merge(df, res, how='inner', on='subject id', sort=False, copy=False)
		merged.to_csv(outfile, sep='\t', index=False)
		return merged


if __name__ == '__main__':
	xmlparse = ParseXML('F0YAA561014-Alignment.xml')
	res = xmlparse.getRes('acc_anno.txt')
	csvparse = ParseCSV('F0YAA561014-Alignment-HitTable.csv')
	merged = csvparse.mergeRes(res, 'merged.txt')