[英]Generate and execute R, Python, etc.., script from within bash script
I have been trying to find a solution for this for a while but haven't found anything satisfactory yet. 我一直试图找到一个解决方案一段时间,但还没有找到任何令人满意的。 I write a lot of bash scripts, but sometimes I want to use R or Python as part of the script.
我编写了很多bash脚本,但有时我想使用R或Python作为脚本的一部分。 Right now, I end up having to write two scripts;
现在,我最终不得不写两个脚本; the original bash script to perform the first half of the task, and the R or Python script to perform the second half of the task.
原始bash脚本执行任务的前半部分,而R或Python脚本执行后半部分任务。 I call the R/Python script from within the bash script.
我在bash脚本中调用R / Python脚本。
I am not satisfied with this solution because it splits my program over two files, which increases the chances of things getting out of sync, more files to track, etc.. Is there a way to write a block of text that contains the entirety of my R/Python script, and then have bash spit it out into a file and pass arguments to it & execute it? 我对这个解决方案不满意,因为它将我的程序分成两个文件,这增加了事情不同步的机会,更多的文件跟踪等等。有没有办法写一个包含整个文件的文本块我的R / Python脚本,然后将bash吐出到一个文件中并将参数传递给它并执行它? Is there an easier solution?
有更简单的解决方案吗? This is more complicated than passing simple one-liners to R/Python because it usually involves creating and manipulating objects over several steps.
这比将简单的单行传递给R / Python更复杂,因为它通常涉及通过几个步骤创建和操作对象。
There are probably lots of solutions, but this one works: 可能有很多解决方案,但这个有效:
#!/bin/bash
## do stuff
R --slave <<EOF
## R code
set.seed(101)
rnorm($1)
EOF
If you want the flexibility to pass additional bash arguments to R, I suggest: 如果你想灵活地将额外的bash参数传递给R,我建议:
#!/bin/bash
## do stuff
R --slave --args $@ <<EOF
## R code
set.seed(101)
args <- as.numeric(commandArgs(trailingOnly=TRUE))
do.call(rnorm,as.list(args))
EOF
obviously you could relax these, eg refer to parameters positionally 显然你可以放松这些,例如在位置参考参数
Here's an example for python, similar to Ben Bolker 's answer 这是python的一个例子,类似于Ben Bolker的回答
#!/bin/bash
python << EOF
print 'Hello $1'
EOF
output: 输出:
> sh test.sh "world"
Hello world
You can pass variables from bash to python too: 你也可以将变量从bash传递给python:
for ((i=1;i<=$1;i++)) do
python << EOF
print 'Hello world $i times'
EOF
done
output: 输出:
> sh test.sh 5
Hello world 1 times
Hello world 2 times
Hello world 3 times
Hello world 4 times
Hello world 5 times
Importing pandas, numpy, matplotlib, and others for normal jobs works fine. 为正常工作导入pandas,numpy,matplotlib和其他工作正常。
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