[Biopython] Bio.Application now subprocess?

[Vincent Davis]

Let me say it was late at night when I started reading thorough this and I
am very new to it so....
The first function defines in Bio/Applications.py
def generic_run(commandline):
"""Run an application with the given commandline (DEPRECATED)......We now
recommend you invoke subprocess directly, using
str(commandline)............."""

The second
class ApplicationResult:
""""""Make results of a program available through a standard interface
(DEPRECATED)................."""

I think these should be moved tp the bottom if possible maybe below a
comment section that indicates the item below are or are going to be
deprecated.

The last line in
class AbstractCommandline(object):
""".......................
You would typically run the command line via a standard Python operating
    system call (e.g. using the subprocess module)."""

I started to read though this example but thought I would read more about
subprocess module, At this point it is not clear to me what bio/Applications
is doing for me. subprocess seems simple. But I  have a lot to learn and I
assume that if I start by getting basic functionality with subprocess then
it will make more sence

One of the parts that is not clear to me is for example in Emboss
class WaterCommandline(_EmbossCommandLine):
..........
self.parameters = \
         [_Option(["-asequence","asequence"], ["input", "file"], None,
1, "First sequence to align")

Not really sure where the parts to the _option line are documented, I assume
in the ...for p in parameters:......
Just not clear, I guess I need to study it more.


  *Vincent Davis
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vincent at vincentdavis.net
 my blog <http://vincentdavis.net> |
LinkedIn<http://www.linkedin.com/in/vincentdavis>


On Sat, Apr 10, 2010 at 4:28 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Sat, Apr 10, 2010 at 6:43 AM, Vincent Davis <vincent at vincentdavis.net>
> wrote:
> > I was considering writing a module for using the command line Affymetrix
> > Power Tools Software
> > LINK<
> http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx
> >
> > Mostly
> > to convert between CEL file types but there are lots of other features
> > <
> http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx
> >If
> > I read correctly will be replaced using subprocess. Are there any modules
> > currently using subprcess rather than Bio.Application?
> > Anything I should know but don't (as if you know what I know) or consider
>
> Hi Vincent,
>
> The idea is to use a Bio.Application based wrapper to build a command
> line string, and invoke that with the subprocess module (i.e. use BOTH).
> The tutorial has several examples of this (e.g. alignment tools and BLAST).
>
> What have you been reading that makes you think Bio.Application is
> being replaced with subprocess? We should probably clarify it.
>
> Peter
>