[Biopython-dev] ApplicationResult and generic_run obsolete?
Tiago Antão
tiagoantao at gmail.com
Tue Jul 7 08:33:49 UTC 2009
2009/7/6 Peter <biopython at maubp.freeserve.co.uk>:
> The point of this discussion is to agree the "best practice". It
> sounds like this will be telling people to use subprocess for full
> control, but we may continue to provide one or two helper
> functions for very common usecases.
I tried to use Bio.Application and there was one part (maybe I am
using it wrongly) that was kind of awkward: parameters (Ive added my
code below).
The need to declare them explicitly plus the fact that in some cases
parameters are always compulsory and really not parameters (granted a
strange use case, but I have a fixed parameter for genepop, namely
saying that the run is machine-controlled, batch mode).
At the end of the day, I end up with a lot of biolerplate code (like below).
_Argument(["command"],
["INTEGER(.INTEGER)*"],
None,
True,
"GenePop option to be called"),
_Argument(["mode"],
["Dont touch this"],
None,
True,
"Should allways be batch"),
_Argument(["input"],
["input"],
None,
True,
"Input file"),
_Argument(["Dememorization"],
["input"],
None,
False,
"Dememorization step"),
_Argument(["BatchNumber"],
["input"],
None,
False,
"Number of MCMC batches"),
_Argument(["BatchLength"],
["input"],
None,
False,
"Length of MCMC chains"),
_Argument(["HWtests"],
["input"],
None,
False,
"Enumeration or MCMC"),
--
"A man who dares to waste one hour of time has not discovered the
value of life" - Charles Darwin
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