[Biojava-l] library for running blast and formatdb
Schreiber, Mark
mark.schreiber@agresearch.co.nz
Tue, 14 Jan 2003 14:07:37 +1300
Wouldn't be a bad place to start anyway.
- Mark
> -----Original Message-----
> From: Francois Pepin [mailto:francois.pepin@mail.mcgill.ca]
> Sent: Tuesday, 14 January 2003 2:00 p.m.
> To: Schreiber, Mark; 'Patrick McConnell'
> Cc: biojava-l@biojava.org
> Subject: RE: [Biojava-l] library for running blast and formatdb
>
>
> I have some code for the running part of it (as java is
> pretty finicky about running external apps) on almost any OS.
>
> It's pretty simple (you have to send it the string to be
> run), but it's pretty robust and can capture the outputs
> properly for later use.
>
> If people think that it would be useful to have something of
> the kind String goes in, Stream goes out, I'll be happy to
> set it up so that it's flexible and releasable.
>
> Then if someone wants to do something fancy with it, it'll be
> all ready to go.
>
> Francois
>
> -----Original Message-----
> From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]
> On Behalf Of Schreiber, Mark
> Sent: 13 janvier, 2003 15:08
> To: Patrick McConnell
> Cc: biojava-l@biojava.org
> Subject: RE: [Biojava-l] library for running blast and formatdb
>
>
> One thing sorely missing from BioJava is the ability to
> launch and capture the results of common bioinformatics
> programs. I know Java isn't the best at this but it's not
> that bad. It's also needed if you want to develop pipeline
> type applications.
>
> Would it be possible to get some kind of over-arching
> interface based API so that services can be made available
> with similar interfaces.
>
> Possibly a Service or Program interface a Paramater list or
> map, some kind of result stream?
>
> Just my $0.02
>
> - Mark
>
> > -----Original Message-----
> > From: Patrick McConnell [mailto:MCCon012@mc.duke.edu]
> > Sent: Tuesday, 14 January 2003 4:15 a.m.
> > To: biojava-l@biojava.org
> > Subject: Re: [Biojava-l] library for running blast and formatdb
> >
> >
> >
> >
> > >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?
> >
> > The CLI project looks like it is quite flexible and robust.
> But, with
> > this, it is somewhat complex. This is in contrast to the
> simplicity
> > of creating parameters via reflection. I think that these
> two methods
> > could be effectively combined so that we gain the simplicty of
> > reflection with the flexibility of CLI. The base
> parameters class can
> > use CLI to build its parameters. As an option, it can build CLI
> > options via reflection for simplicity. When users extend the base
> > class, they can utilize the flexibility of CLI if they need it,
> > otherwise they can use reflection for a quick and dirty
> > parameter parsing. The base class could even extend the
> > Options class, so we are really working with a hybrid of the
> > two. What does everyone think?
> >
> > -Patrick
> >
> >
> >
> >
> >
> >
> > "Michael L. Heuer" <heuermh@acm.org>@shell3.shore.net> on
> 01/10/2003
> > 05:18:52 PM
> >
> > Sent by: Michael Heuer <heuermh@shell3.shore.net>
> >
> >
> > To: Patrick McConnell <MCCon012@mc.duke.edu>
> > cc: biojava-l@biojava.org
> >
> > Subject: Re: [Biojava-l] library for running blast and formatdb
> >
> >
> > 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
> > >
> > >
> > > _______________________________________________
> > > Biojava-l mailing list - Biojava-l@biojava.org
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list - Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
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