使用 python itertools.groupby 解析文本数据块

Question

我正在尝试使用 itertools.groupby 解析 python 2.7 中的一段文本数据具有以下结构：

BEGIN IONS
TITLE=cmpd01_scan=23
RTINSECONDS=14.605
PEPMASS=694.299987792969 505975.375
CHARGE=2+
615.839727 1760.3752441406
628.788226 2857.6264648438
922.4323436 2458.0959472656
940.4432533 9105.5
END IONS
BEGIN IONS
TITLE=cmpd01_scan=24
RTINSECONDS=25.737
PEPMASS=694.299987792969 505975.375
CHARGE=2+
575.7636234 1891.1656494141
590.3553938 2133.4477539063
615.8339562 2433.4252929688
615.9032114 1784.0628662109
END IONS

我需要从以 "TITLE="、"PEPMASS="、"CHARGE=".

开头的行中提取信息

我使用的代码如下：

import itertools
import re

data_file='Test.mgf'
def isa_group_separator(line):
    return line=='END IONS\n'

regex_scan = re.compile(r'TITLE=')
regex_precmass=re.compile(r'PEPMASS=')
regex_charge=re.compile(r'CHARGE=')


with open(data_file) as f:
    for (key,group) in itertools.groupby(f,isa_group_separator):
        #print(key,list(group)) 
        if not key:
            precmass_match = filter(regex_precmass.search,group)
            print precmass_match            

            scan_match= filter(regex_scan.search,group)
            print scan_match

            charge_match = filter(regex_charge.search,group)
            print charge_match

然而，输出只获取"PEPMASS="行，如果'scan_match'赋值在'precmass_match'之前完成，则只打印"TITLE="行；

> ['PEPMASS=694.299987792969 505975.375\n'] [] []
> ['PEPMASS=694.299987792969 505975.375\n'] [] []

有人可以指出我在这里做错了什么吗？

Answer 1

我可能会尝试以这种方式解析（不使用 groupby(

import re

file = """\
BEGIN IONS
TITLE=cmpd01_scan=23
RTINSECONDS=14.605
PEPMASS=694.299987792969 505975.375
CHARGE=2+
615.839727 1760.3752441406
628.788226 2857.6264648438
922.4323436 2458.0959472656
940.4432533 9105.5
END IONS
BEGIN IONS
TITLE=cmpd01_scan=24
RTINSECONDS=25.737
PEPMASS=694.299987792969 505975.375
CHARGE=2+
575.7636234 1891.1656494141
590.3553938 2133.4477539063
615.8339562 2433.4252929688
615.9032114 1784.0628662109
END IONS""".splitlines()

pat = re.compile(r'(TITLE|PEPMASS|CHARGE)=(.+)')
data = []

for line in file:
    m = pat.match(line)
    if m is not None:
        if m.group(1) == 'TITLE':
            data.append([])
        data[-1].append(m.group(2))

print(data)

打印：

[['cmpd01_scan=23', '694.299987792969 505975.375', '2+'], ['cmpd01_scan=24', '694.299987792969 505975.375', '2+']]

Answer 2

原因是group是一个迭代器，它只运行一次。请找到完成这项工作的修改后的脚本。

import itertools
import re

data_file='Test.mgf'


def isa_group_separator(line):
    return line == 'END IONS\n'


regex_scan = re.compile(r'TITLE=')
regex_precmass = re.compile(r'PEPMASS=')
regex_charge = re.compile(r'CHARGE=')


with open(data_file) as f:
    for (key, group) in itertools.groupby(f, isa_group_separator):
        if not key:
            g = list(group)

            precmass_match = filter(regex_precmass.search, g)
            print precmass_match

            scan_match = filter(regex_scan.search, g)
            print scan_match

            charge_match = filter(regex_charge.search, g)
            print charge_match

使用 python itertools.groupby 解析文本数据块

Parsing blocks of text data with python itertools.groupby

python

text-parsing

itertools