[Biojava-l] library for running blast and formatdb
Michael L. Heuer
Fri, 10 Jan 2003 17:18:52 -0500 (EST)
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
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
but they don't have any extra support for external programs.
> 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
> Biojava-l mailing list - Biojavafirstname.lastname@example.org