从 R 脚本运行 bash 脚本
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Run a bash script from an R script
提问by cianius
So I have this programme samtools that I want to use from cmd line, converting one file to another. It works like this:
所以我有这个程序 samtools，我想从 cmd 行使用它，将一个文件转换为另一个文件。它是这样工作的：
bash-4.2$ samtools view filename.bam | awk '{OFS="\t"; print ">""\n"}' - > filename.fasta
As I want to automate this, I would like to automate it by using an R script. I know you can use system() to run an OS command, but I cannot get it to work by trying
由于我想自动执行此操作，因此我想使用 R 脚本来自动执行此操作。我知道您可以使用 system() 来运行操作系统命令，但我无法通过尝试使其工作
system(samtools view filename.bam | awk '{OFS="\t"; print ">""\n"}' - > filename.fasta)
Is it just a matter of using regexes to get rid of spaces and stuff so the comma nd argument system(command) is readable? How do I do this?
是否只是使用正则表达式摆脱空格和东西以便命令参数系统（命令）可读的问题？我该怎么做呢？
EDIT:
编辑：
system("samtools view filename.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > first_batch_1.fasta") Error: unexpected input in "system("samtools view filename.bam | awk '{OFS="\"
system("samtools 查看文件名.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > first_batch_1.fasta") 错误："system("samtools 查看文件名) 中有意外输入.bam | awk '{OFS="\"
EDIT2:
编辑2：
system("samtools view filename.bam | awk '{OFS=\"\t\"; print \">\"$1\"\n\"$10}' - > filename.fasta")
system("samtools 查看文件名.bam | awk '{OFS=\"\t\"; print \">\"$1\"\n\"$10}' -> filename.fasta")
awk: cmd. line:1: {OFS=" "; print ">""
awk: cmd. line:1: ^ unterminated string
awk: cmd. line:1: {OFS=" "; print ">""
awk: cmd. line:1: ^ syntax error
>
EDIT3: And the winner is:
EDIT3：获胜者是：
system("samtools view filename.bam | awk '{OFS=\"\t\"; print \">\"\"\n\"}' -> filename.fasta")
回答by Andrie
The way to debug this is to use catto test whether your character string has been escaped correctly. So:
调试这个的方法是用来cat测试你的字符串是否被正确转义。所以：
- Create an object
xwith your string - Carefully escape all the special characters, in this case quotes and backslashes
- Use
cat(x)to inspect the resulting string.
x用你的字符串创建一个对象- 小心地转义所有特殊字符，在这种情况下是引号和反斜杠
- 使用
cat(x)检查结果字符串。
For example:
例如：
x <- 'samtools view filename.bam | awk \'{OFS="\t"; print ">""\n"}\' - > filename.fasta'
cat(x)
samtools view filename.bam | awk '{OFS="\t"; print ">""\n"}' - > filename.fasta
If this gives the correct string, then you should be able to use
如果这给出了正确的字符串，那么您应该能够使用
system(x)
