我有一个路径文件叫做test.txt
/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
注意行数是偶数并且总是偶数，我的最终目标是解析这个文件并创建一个新的以2 × 2为基础遍历这些路径的文件。我在尝试enumerate函数，但这不会解析成2对2。此外，我将超出范围，因为我所做的索引方式是错误的。如果有人能告诉我如何正确地索引enumerate，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]))
结果如下:
{"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，因为它正在经历我的路径的每个元素，即gr等，而不是打印下一个路径。对于第一次迭代，下一个打印的路径应该是:"fastq_2":"/groups/cgsd/javed/validation_set/LeungSY_Targeted_SS-190528-01a/Clean/pfg001G_2_Clean.fastq.gz".
我相信这个问题本身可以用itertools更优雅地解决，我只是不知道怎么做。如果有人能告诉我枚举索引是否也可以工作，那就太好了。
一个问题是，您试图在之前从对的第二行访问数据。另外，您不能使用line[index + 1]访问第二行，因为它指向当前行的字符，而不是尚未读取的下一行。
所以你需要跟踪行对。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)。读取第一行时存储fastq_1的名称和路径。只在第二行写入输出。这样的:
进口re
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新行字符。
@mhawke已经提供了一个很好的解决方案，但是要给出另一种方法，"循环遍历这些…在二乘二的基础上;可以使用more_itertools库中的more_itertools.chunked函数或Python手册中的grouper()配方来完成。
这也提供了当最后一行是奇数行时应该发生什么的选项;是否会引发错误或将其与默认值配对。
你可能想要考虑当你给变量分配索引时，你得到的是该字符串的索引字符，而不是它的索引。
你所能做的就是将e文件分配给一个列表，然后获得索引位置，这样你就可以在你想要的行之间切换。
还是不明白点，你是想在fastq_1和fastq_2的行之间切换，还是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
{"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]