[Biopython-dev] subprocess and calling application wrappers

[Peter]

On Tue, Jun 1, 2010 at 4:15 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Jun 1, 2010 at 2:23 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>> I'd suggest having an option to not capture stdout and stderr, which
>> would help users avoid those cases where a program spews a lot to
>> stdout and it's unwieldy to capture and stick it into a string.
>
> We need to avoid any risk of deadlocks, so I guess the safe
> implementation here would be call subprocess with stdout and
> stderr sent to dev null.

How does this look? Tested on Mac and Windows:
http://github.com/peterjc/biopython/tree/app-exec2

Example usage without capturing the output:

    from Bio.Emboss.Applications import WaterCommandline
    water_cmd = WaterCommandline(gapopen=10, gapextend=0.5, stdout=True,
                                 asequence="a.fasta", bsequence="b.fasta")
    print "About to run:\n%s" % water_cmd
    return_code = water_cmd()
    print "Return code: %i" % return_code

Example usage with stdout and stderr capture:

    from Bio.Emboss.Applications import WaterCommandline
    water_cmd = WaterCommandline(gapopen=10, gapextend=0.5, stdout=True,
                                 asequence="a.fasta", bsequence="b.fasta")
    print "About to run:\n%s" % water_cmd
    stdout, stderr, return_code = water_cmd(capture=True)
    print "Return code: %i" % return_code
    print "Tool output:\n%s" % stdout

Note in this implementation it either returns an integer error level
(the default) or a tuple of stdout, stderr and the error level return
code. If we opt for adding methods rather than using __call__
these could be different methods instead.

Another potentially useful option would be to copy the
subprocess.check_call() function in Python 2.5+ which verifies
the return code (error level) is zero and raises an exception if not
(probably only sensible if not capturing the output?). Maybe this
could even be the default behaviour?

[I would prefer to keep the interface as simple as possible though,
less options is better! KISS principle.]

Peter