[Biojava-l] library for running blast and formatdb

[Michael L. Heuer]

On Fri, 10 Jan 2003, Patrick McConnell wrote:

> In the process, I developed some useful and flexible base classes for
> formatting parameters and running programs.  Parameters are automatically
> converted to an argument array via reflection and reading of standard out
> and standard error in separate threads is handled automatically.

The base classes are nice, but I prefer the design of

> http://jakarta.apache.org/commons/cli

a lot better for handling parameters.

I suppose it's a matter of another external dependency vs. reinvented
utility code in biojava . . .  Would it make sense to merge the better
qualities of the two?

I also have a few simple classes for oneoff scripts with command line &
logging facade support that I use all the time, see

> http://www.shore.net/~heuermh/oneoff.tar.gz

but they don't have any extra support for external programs.

   michael

>
> Check it out if you are interested:
> http://www.dbsr.duke.edu/software/blast/default.htm .  The full source,
> javadocs, and binary class files are available.  Also, if this seems
> appropriate for BioJava, I have no problem donating it to the cause.  I
> think that at least the base classes, or some modification of them, would
> be useful to others.
>
> Please email me with suggestions/comments,
>
> -Patrick McConnell
> Duke Bioinformatics Shared Resource
> mccon012@mc.duke.edu
>
>
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