python 遍历文件时枚举超出范围

Question

我有一个名为 test.txt

的路径文件

/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001G_1_Clean.fastq.gz
/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001G_2_Clean.fastq.gz
/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001T_1_Clean.fastq.gz
/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001T_2_Clean.fastq.gz
/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002G_1_Clean.fastq.gz
/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002G_2_Clean.fastq.gz
/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002T_1_Clean.fastq.gz
/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002T_2_Clean.fastq.gz

请注意，行数是偶数且始终是偶数，我的最终目标是解析此文件并创建一个新文件，以两两方式循环遍历这些路径。我正在尝试 enumerate 函数，但这不会两个两个地解析。此外，我超出了范围，因为索引我正在做的方式是错误的。如果有人可以告诉我如何使用 enumerate.

正确索引，那也很棒

 with open('./src/test.txt') as f:
    for index,line in enumerate(f):
        sample = re.search(r'pfg[\dGT]+',line)
        sample_string = sample.group(0)
        #print(sample_string)
        print('{{"name":"{0}","readgroup":"{0}","platform_unit":"{0}","fastq_1":"{1}","fastq_2":"{2}","library":"{0}"}},'.format(sample_string,line,line[index+1]))

结果是这样的：

{"name":"pfg001G","readgroup":"pfg001G","platform_unit":"pfg001G","fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001G_1_Clean.fastq.gz
","fastq_2":"g","library":"pfg001G"},
{"name":"pfg001G","readgroup":"pfg001G","platform_unit":"pfg001G","fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001G_2_Clean.fastq.gz
","fastq_2":"r","library":"pfg001G"},
{"name":"pfg001T","readgroup":"pfg001T","platform_unit":"pfg001T","fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001T_1_Clean.fastq.gz
","fastq_2":"o","library":"pfg001T"},
{"name":"pfg001T","readgroup":"pfg001T","platform_unit":"pfg001T","fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001T_2_Clean.fastq.gz
","fastq_2":"u","library":"pfg001T"},
{"name":"pfg002G","readgroup":"pfg002G","platform_unit":"pfg002G","fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002G_1_Clean.fastq.gz
","fastq_2":"p","library":"pfg002G"},
{"name":"pfg002G","readgroup":"pfg002G","platform_unit":"pfg002G","fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002G_2_Clean.fastq.gz
","fastq_2":"s","library":"pfg002G"},
{"name":"pfg002T","readgroup":"pfg002T","platform_unit":"pfg002T","fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002T_1_Clean.fastq.gz
","fastq_2":"/","library":"pfg002T"},
{"name":"pfg002T","readgroup":"pfg002T","platform_unit":"pfg002T","fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002T_2_Clean.fastq.gz","fastq_2":"c","library":"pfg002T"},

显然索引是错误的，因为它遍历了我路径中的每个元素，即 g r 等，而不是打印下一个路径。对于第一次迭代，打印的下一个路径应该是："fastq_2":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001G_2_Clean.fastq.gz".

我相信问题本身可以用 itertools 更优雅地解决，我只是不知道该怎么做。如果有人可以告诉我枚举索引是否也可以工作，那也很棒。

Answer 1

一个问题是您在阅读数据对之前试图从第二行访问数据。此外，您不能使用 line[index + 1] 访问第二行，因为它指的是当前行中的一个字符，而不是尚未读取的下一行。

因此您需要跟踪成对的行。您可以使用 enumerate() 提供的索引来确定当前行是第一行（因为它是偶数）还是第二行（因为它是奇数）。当您阅读第一行时，存储 fastq_1 的名称和路径。只在第二行写输出。像这样：

重新导入

with open('test.txt') as f:
    for index, line in enumerate(f):
        if index % 2 == 0:      # even, so this is the first line of a pair
            name = re.search(r'pfg[\dGT]+',line).group(0)
            fastq_1 = line.rstrip()
        else:                   # odd, so second line. Emit result
            fastq_2 = line.rstrip()
            print('{{"name":"{0}","readgroup":"{0}","platform_unit":"{0}","fastq_1":"{1}","fastq_2":"{2}","library":"{0}"}},'.format(name, fastq_1, fastq_2))

line.rstrip() 需要删除每行末尾的尾随换行符。

Answer 2

您可能需要考虑，当您将索引分配给变量时，您得到的是该字符串的索引字符而不是它的索引。

你可以做的是将文件分配给一个列表，然后获取索引位置，这样你就可以根据需要在行之间切换。

还是不明白点，你是想在fastq_1和fastq_2两行之间切换还是每条路径都根据它的key？

代码语法

with open(path) as f:
    lis = list(f)
    for index, line in enumerate(lis):
        try:
            sample = re.search(r'pfg[\dGT]+',line)
            sample_string = sample.group(0)

            print(f'{{"name":"{sample_string}","readgroup":"{sample_string}","platform_unit":"{sample_string}","fastq_1":"{line}","fastq_2":"{lis[index+1]}","library":"{sample_string}"}},')
        except IndexError:
                break

输出

{"name":"pfg001G","readgroup":"pfg001G","platform_unit":"pf
g001G","fastq_1":"/groups/cgsd/javed/validation_set/Leung
SY_Targeted_SS-190528-01a/Clean/pfg001G_1_Clean.fastq.gz
","fastq_2":"/groups/cgsd/javed/validation_set/LeungSY_Ta
rgeted_SS-190528-01a/Clean/pfg001G_2_Clean.fastq.gz
","library":"pfg001G"},
{"name":"pfg001G","readgroup":"pfg001G","platform_unit":"pf
g001G","fastq_1":"/groups/cgsd/javed/validation_set/Leung
SY_Targeted_SS-190528-01a/Clean/pfg001G_2_Clean.fastq.gz
","fastq_2":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001T_1_Clean.fastq.gz
","library":"pfg001G"},
{"name":"pfg001T","readgroup":"pfg001T","platform_unit":"pf
g001T","fastq_1":"/groups/cgsd/javed/validation_set/Leung
SY_Targeted_SS-190528-01a/Clean/pfg001T_1_Clean.fastq.gz
","fastq_2":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001T_2_Clean.fastq.gz
","library":"pfg001T"},
{"name":"pfg001T","readgroup":"pfg001T","platform_unit":"pf
g001T","fastq_1":"/groups/cgsd/javed/validation_set/Leung
SY_Targeted_SS-190528-01a/Clean/pfg001T_2_Clean.fastq.gz
","fastq_2":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002G_1_Clean.fastq.gz
","library":"pfg001T"},
{"name":"pfg002G","readgroup":"pfg002G","platform_unit":"pf
g002G","fastq_1":"/groups/cgsd/javed/validation_set/Leung
SY_Targeted_SS-190528-01a/Clean/pfg002G_1_Clean.fastq.gz
","fastq_2":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002G_2_Clean.fastq.gz
","library":"pfg002G"},
{"name":"pfg002G","readgroup":"pfg002G","platform_unit":"pf
g002G","fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002G_2_Clean.fastq.gz
","fastq_2":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002T_1_Clean.fastq.gz
","library":"pfg002G"},
{"name":"pfg002T","readgroup":"pfg002T","platform_unit":"pfg002T","fastq_1":"/groups/cgsd/javed/validation_set/Leung
SY_Targeted_SS-190528-01a/Clean/pfg002T_1_Clean.fastq.gz
","fastq_2":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002T_2_Clean.fastq.gz
","library":"pfg002T"},

[Program finished]

Answer 3

@mhawke 已经提供了一个很好的解决方案，但要给出另一种方法，“循环遍历这些......在两个基础上”可以使用 Python 中的 more_itertools.chunked function from the more_itertools library or with the grouper() recipe 来完成手册。

这还提供了当最后一行是奇数行时应该发生什么的选项；是否应该引发错误或将其与默认值配对。

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