[Bioperl-l] what to do about Blast.pm, parsing

Aaron J Mackey ajm6q@virginia.edu
Tue, 16 Jan 2001 18:25:13 -0500 (EST)

On Tue, 16 Jan 2001, Jason Stajich wrote:

> I also have been playing with Parse::RecDescent some.  While writing a
> grammar is not the most fun I've ever had, I've been able to write a
> parser for GenBank files and get at least accession,locus, and sequence
> lines parsed (I know, big deal).  Feature table will be a bit more fun,
> but I think it may be a useful exercise whether or not we will really just
> write grammars for seqformats I don't know.  Perhaps a grammar could be
> written for blast files - might be more trouble than it's worth...

I've often thought the same (and then stepped back and wondered if
blast/fasta/hmmer output could be expressed in BNF [ Backus-Naur Form ]).
It seems like an excellent project for an undergrad CS major who wanted to
crossover into bioinformatics.  There's too much grunt work involved for
any of us to want to do it, though ;)  Maybe we should take this off-list
Jason, but do you have any comments on Parse::ResDecent vs. Parse::Yapp


 o ~   ~   ~   ~   ~   ~  o
/ Aaron J Mackey           \
\  Dr. Pearson Laboratory  /
 \ University of Virginia  \
 /  (804) 924-2821          \
 \  amackey@virginia.edu    /
  o ~   ~   ~   ~   ~   ~  o