os.system calls to other modules

Question

os.system calls to other modules

crashfrog opened this issue 7 years ago · comments

Hi guys,

This:

os.system("python2.7 "+dirpath+"/libs/mapping_and_assembly_hybrid.py H_and_O_and_specific_genes.fasta "+mapping_mode+" "+str(threads)+" "+fnameA+" "+fnameB)

is an, um, surprising way to call Python modules from within a Python script. Is there a reason you're not simply importing the other modules? For starters, this makes you needlessly dependent on old versions of Python; it's also extremely fragile and non-standard; lastly it's almost totally incompatible with the Python packaging ecosystem. (As a bonus, subprocess.check_call is quite a bit preferable to os.system for making subshell calls, but there's never a need to subshell-call Python from Python.)

Would you accept a PR that addressed some of these issues?

Justin Payne
Bioinformatician
US Food and Drug Administration

Shaokang Zhang · Answer 1 · Tue Dec 05 2017 00:11:26 GMT+0800 (China Standard Time)

Hi Justin,

Thanks for your suggestions. I am an amateur programmer who learned python all by myself. I know that there are many unprofessional parts in my code. It would be great that you are willing to help me to fix it.
Yes, we will accept a PR to address those issues.

Regards,
Shaokang

Justin Payne · Answer 2 · Tue Dec 05 2017 03:12:05 GMT+0800 (China Standard Time)

Cool, no sweat. I'll fork the repo and have a PR for you later this week. I'll try to annotate the changes I'm making in the commit messages and comments.

Thanks!

Henk den Bakker · Answer 3 · Tue Dec 05 2017 03:37:46 GMT+0800 (China Standard Time)

Hi Justin, Are you planning on making any other changes? I have a fork where I made SeqSero2 version independent (runs both python 2 and 3) and you have a choice between the classic output or tab delimited output.

…

-Henk

On Mon, Dec 4, 2017 at 2:12 PM, Justin Payne ***@***.***> wrote: Cool, no sweat. I'll fork the repo and have a PR for you later this week. I'll try to annotate the changes I'm making in the commit messages and comments. Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AND_dFzD1guG8XWKjrmJjRps8wjExvTnks5s9EQFgaJpZM4Q0xQx> .

Torsten Seemann · Answer 4 · Tue Sep 04 2018 12:05:52 GMT+0800 (China Standard Time)

@hcdenbakker where is your version?

Henk den Bakker · Answer 5 · Tue Sep 04 2018 19:59:52 GMT+0800 (China Standard Time)

@tseemann Here it is: https://github.com/hcdenbakker/SeqSero2. Not something I have actively worked recently.