[Biojava-l] library for running blast and formatdb

[Wiepert, Mathieu]

I would love to see this placed in the biojava core...  Might switch me back from bioperl ;-)

-Mat


> -----Original Message-----
> From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> Sent: Friday, January 10, 2003 3:12 PM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] library for running blast and formatdb
> 
> 
> 
> 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
> 
> 
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