排序制表符分隔fi

Question

我试图从python调用unix sort命令来排序一个制表符分隔的文件，但我做不到。当我在google上搜索时，我发现在命令中添加-t$'\t'是有效的，当我试图从shell中进行排序时，我也为我工作，但是当我尝试从python中进行排序时，它就不起作用了。在

这就是我在剧本中尝试的

tabdel="$'\t'"
sort_file_cmd="sort -t {1} -k2,2 -k6,6n {0}".format(file_to_be_sorted.name,tabdel)
print sort_file_cmd,shlex.split(sort_file_cmd)
subprocess.call(sort_file_cmd,stdout=sort_bt,shell=True)

print sort_file_cmd将打印此文件

^{pr2}$

当从shell运行时，它工作得很好，但是在python脚本中运行时会产生sort:multi-character tab'$\t'错误

我如何克服这个问题？在

样本数据

gi|52317161|ref|NM_001004713.1| Homo sapiens olfactory receptor, family 1, subfamily I, member 1 (OR1I1), mRNA  gnl|BL_ORD_ID|10980 gi|58801268|ref|NP_001011737.1| olfactory receptor 1357 [Mus musculus]  3071921 1   307 1.90237e-150    1108.0  
gi|52317161|ref|NM_001004713.1| Homo sapiens olfactory receptor, family 1, subfamily I, member 1 (OR1I1), mRNA  gnl|BL_ORD_ID|460 gi|22129025|ref|NP_667153.1| olfactory receptor 351 [Mus musculus]    302 10  915 2   303 5.70073e-105    806.0  
gi|52317161|ref|NM_001004713.1| Homo sapiens olfactory receptor, family 1, subfamily I, member 1 (OR1I1), mRNA  gnl|BL_ORD_ID|4490 gi|33238878|ref|NP_666817.1| olfactory receptor 24 [Mus musculus]    308 1   921 1   307 9.58658e-105    805.0  
gi|52317161|ref|NM_001004713.1| Homo sapiens olfactory receptor, family 1, subfamily I, member 1 (OR1I1), mRNA  gnl|BL_ORD_ID|458 gi|22129031|ref|NP_667152.1| olfactory receptor 353 [Mus musculus]    302 10  915 2   303 1.01585e-103    798.0  
gi|52317161|ref|NM_001004713.1| Homo sapiens olfactory receptor, family 1, subfamily I, member 1 (OR1I1), mRNA  gnl|BL_ORD_ID|13639 gi|268837230|ref|NP_667200.2| olfactory receptor 1496 [Mus musculus]    3071921 3   309 1.50986e-99 771.0  
gi|52317161|ref|NM_001004713.1| Homo sapiens olfactory receptor, family 1, subfamily I, member 1 (OR1I1), mRNA  gnl|BL_ORD_ID|13345 gi|283837936|ref|NP_666450.2| olfactory receptor 374 [Mus musculus] 310 1   930 1   310 4.18033e-99 768.0  
gi|52317161|ref|NM_001004713.1| Homo sapiens olfactory receptor, family 1, subfamily I, member 1 (OR1I1), mRNA  gnl|BL_ORD_ID|455 gi|22129035|ref|NP_667150.1| olfactory receptor 354 [Mus musculus]    302 13  918 8   309 1.85488e-98 764.0  
gi|52317161|ref|NM_001004713.1| Homo sapiens olfactory receptor, family 1, subfamily I, member 1 (OR1I1), mRNA  gnl|BL_ORD_ID|410 gi|22129071|ref|NP_667122.1| olfactory receptor 1377 [Mus musculus]   305 1   915 1   304 3.06622e-97 755.0  
gi|52317161|ref|NM_001004713.1| Homo sapiens olfactory receptor, family 1, subfamily I, member 1 (OR1I1), mRNA  gnl|BL_ORD_ID|312 gi|53933206|ref|NP_001005569.1| olfactory receptor 366 [Mus musculus] 307 1   921 1   307 2.14345e-96 749.0  
gi|52317161|ref|NM_001004713.1| Homo sapiens olfactory receptor, family 1, subfamily I, member 1 (OR1I1), mRNA  gnl|BL_ORD_ID|4458 gi|58801284|ref|NP_001011748.1| olfactory receptor 867 [Mus musculus]    3091927 1   309 7.36974e-96 748.0   

Answer 1

$' '引用语法由shell解释。在

你需要说：

tabdel=r'\t'

Answer 2

您可以避免使用shell=True，只需使用list而不是字符串作为命令：

>>> subprocess.call(['sort', '-t', '\t', 'testing.txt'])
a       b
c       d
0

不要构建单个流，而是使用一个字符串列表，每个字符串代表原始命令中的一个令牌。在您的情况下，完整的“命令行”将是：

^{pr2}$

注意，这种方法更安全，您应该尽量避免{}。只有当您想使用一些shell功能时，您才必须使用shell=True，如内置命令ifs、循环、管道（尽管这些可以是构建使用subprocess.Popen…）等。在所有只想执行传递一些参数的命令的情况下，shell=True是可以避免的。在

您可以使用shlex.split从命令字符串获取字符串列表：

>>> cmdline = shlex.split("sort -t '\t' -k2,2 -k6,6n")
>>> cmdline
['sort', '-t', '\t', '-k2,2', '-k6,6n']
>>> cmdline.append(file_to_be_sorted.name)   # insert the last argument.

注意，在本例中，必须在原始字符串中用单引号将\t括起来。在

---

如果您仍然想使用shell=True，那么只需使用$'\t'转义：

>>> subprocess.call("sort -t '\t' testing.txt", shell=True)
a       b
c       d
0

对我来说很好。在