[Biojava-l] library for running blast and formatdb

[Patrick McConnell]

In the past, there have been quite a few requests on how to run blast from
a Java program.  I have developed some classes for running NCBI blastall
and formatdb.  All of the parameters for the respective programs are
implemented, and everything is reasonably well documented.  Also useful is
an option to run blast without input and output files, utilizing standard
input and output.

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.

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