[Biopython-dev] stdout/stderr handling oddity

[Peter Cock]

Hi all,

While looking at the BWA wrapper from Saket Choudhary
https://github.com/biopython/biopython/pull/167 and the
associated enhancement to the __call__ functionality of the
command line wrapper base class, I wrote a couple of unit
tests - which have left me a little puzzled:

https://github.com/biopython/biopython/commit/3f5d4c442424a7ca33ae0bafa60c840e80ae2fda

Could a few of you try running this test_Application.py
file and confirm it works as is, and try uncommenting the
two problem test cases?

(I'm curious if the echo test works as intended on a plain
Windows machine without cygwin installed - I hope so).

Unless anyone else can explain this, I think the next step
is a simple test program which produces predictable
output to both stdout and stderr, just in case this is due
to there being no stderr output in these tests.

e.g. Print integers 1, 2, 3, 4, ..., to some sensible limit,
like 20, where non-primes are on stdout while primes on
stderr.

Peter