How would I go about calling BWA from a python script?

[prs321]

I am trying to make a python script that reads in a text file of pair end reads and then calls BWA mem on the pairs and outputs SAM files.

[rhinoceros]

Why not just make it a shell script?

script.sh

BWA-MEM $1

sh script.sh yourfile.txt

[dpryan]

os.system, os.popen, os.fork, etc. There are a few different ways to do that, each with their pros and cons.

Edit: As rhinoceros mentions, depending on the amount of processing you want done, this would normally performed via shell script.

[prs321]

I was told specifically to make a python script because it is more stable.

[dpryan]

You can ignore whomever told you that, he/she doesn't have a clue.

Python is more powerful, in that you can certainly do more with it easily, but doing something simple like stitching together a pipeline is often easier to do in a shell script (that's their intended purpose).

There are a lot of tools, learning which ones are most convenient for what situations are an important (and error ridden) part of the learning process.

[liux]

If you have to, use subprocess package. It should work fine.

I think shell script is straightforward, and should be used, if all it does is to run a simple command. But I prefer python when the pipeline is complex.

In my case, it is a little more complicated. In one of pipelines I created in python, I need to submit jobs to clusters. It is so much easier to read run configuration file, parse out sample name, create proper path, make meaningful job name in python (try it in bash script, you will know why I prefer python). However the submitted command errored out when it submitted from python, but pasted the print-out commands in terminal worked fine without any problem. I did not have time to find out a solution, so I let the python script generate a full set of shell commands with all the path, parameters, job dependencies, etc, nicely made, output to a xxxx.sh file, and run the shell script afterward. I probably did it backward, and need to do one extra step, but it did work well. I COULD have done all of it in shell script but then I am not so good at shell script, especially when it comes to text manipulation.

[themerlin]

If you will have future python scripts that will use BWA, then it would be worth the time to create a python function that calls bwa. If it is a one time thing, a shell script should be fine.