[Biojava-l] error: Program ncbi-blastn Version 2.2.17 is not supported

[Mark Schreiber]

For a long time now my feeling has been that we should *only* support
the XML version of blast output.  The other formats are too brittle to
be easy to parse.  I also feel similarly about Genbank, EMBL, etc that
may be an extreme view but the power of generic XML parsers and things
like XPath etc really make these formats look very attractive.

- Mark


On Nov 27, 2007 7:47 PM, Andy Yates <ayates at ebi.ac.uk> wrote:
> I think Groovy have adopted a similar system recently & have guidelines
> for how each module should behave (dependencies, build system etc). This
> enforces the idea that a module whilst not part of the core project must
> behave in the same manner the core does. I do like the idea that we can
> have a core biojava & things get added around it & it might encourage
> other users to start developing their own modules for any
> formats/purpose they want.
>
> Richard Holland wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> >> What format options are there from blast? Just thinking if it supports
> >> CIGAR or something like that are we better providing a parser for that
> >> format & saying that we do not support the traditional blast output?
> >> That said it doesn't help is when that format changes so maybe what is
> >> needed is a way to push out parser changes without requiring a full
> >> biojava release (v3 discussion) ...
> >
> > Exactly! So the modular idea would work nicely here - we could have a
> > blast module and only update that single module (which would be its own
> > JAR) whenever the format changes. In a way, BioJava releases as such
> > would no longer happen, except maybe for some kind of core BioJava
> > module. Everything would be done in terms of individual module+JAR
> > releases instead - one for Genbank, one for BioSQL, one for NEXUS, one
> > for Phylogenetic tools, one for translation/transcription, etc. etc.
> >
> > cheers,
> > Richard
>
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