问题描述
/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的文件，以两两为基础循环遍历这些路径。我正在尝试 enumerate 函数，但这不会两两解析。此外，我超出了范围，因为我正在做的索引方式是错误的。如果有人能告诉我如何使用 enumerate 正确编制索引，那也太好了。
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","fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001G_2_Clean.fastq.gz
","fastq_2":"r",{"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"},"fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001T_2_Clean.fastq.gz
","fastq_2":"u",{"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"},"fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002G_2_Clean.fastq.gz
","fastq_2":"s",{"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"},"fastq_1":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg002T_2_Clean.fastq.gz","fastq_2":"c",显然索引是错误的，因为它遍历了我路径的每个元素，例如 g r 等，而不是打印下一个路径。对于第一次迭代，打印的下一条路径应该是："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。如果有人能告诉我 enumerate 的索引是否也可以工作，那就太好了。
解决方法
一个问题是，您试图在读取数据对之前访问它的第二行中的数据。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。
所以你需要跟踪成对的行。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）。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() 用于删除每行末尾的尾随换行符。
@mhawke 已经提供了一个很好的解决方案，但要提供另一种方法，可以使用 more_itertools 库中的 more_itertools.chunked function 或 {{ 3}} 来自 Python 手册。
这也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。
,您可能需要考虑，当您为变量分配索引时，您获得的是该字符串的索引字符，而不是它的索引。
您可以做的是将文件分配给一个列表，然后获取索引位置，这样您就可以根据需要在行之间切换。
还是没看懂，你是想在fastq_1和fastq_2中的行之间切换还是你每个路径都根据它的键？
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","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
",{"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"},"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
",{"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"},"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
",{"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]