[Biopython] Alternatives to Bio.Application for invoking command line tools?

[Stéphane Téletchéa]

Dear all,

I was about to say the same, my preference for my own projects is always 
to try to rely on upstream development as much as possible, so 
subprocess it the recommandation.

Concerning the pipes, isn't subprocess meant for that already?

According to the doc (https://docs.python.org/3/library/subprocess.html) 
and some answers in stack overflow 
(https://stackoverflow.com/questions/13332268/how-to-use-subprocess-command-with-pipes), 
it should.

Would you have some examples so we can try what is problematic (one/two 
basic cases)?

And yes, thanks for asking for comments :-)

Stéphane

Le 10/05/2020 à 19:09, Peter Cock a écrit :
> Yes, subprocess is very powerful but tricky.
>
> Sadly it doesn't help with giving a nice syntax for building command 
> lines, which for me was the main thing our Bio.Application framework 
> added. Perhaps someone else on the list will have a good suggestion.
>
> Peter

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