[Bioperl-l] Re: SearchIO and GCG

[Jason Stajich]

I've added tests for this now and a test datafile for
t/data/test.gcgblast.

Did you try SearchIO out on any of your files?  I didn't seem to have
any problems with a GCG BLASTP report that I made.

We can't quite parse the hit significance and raw score lines correctly in
the Hit table because the GCGBLAST format wraps the lines weirdly there -
go figure, but the HSPs come out fine.

If you can give it a whirl on some different types of reports like BLASTN
and TBLASTX to make sure we have a complete sweep Steve C or I will
eventually track down the minor parsing issues.

-jason


On Fri, 26 Jul 2002, Peter Kos wrote:

> Jason,
>
> We often hear about RemoteBlast as well as StandaloneBlast using NCBI
> blastall, and sometimes WuBlast is mentioned.
> Can I use SearchIO and Blast.pm for blast outputs of the Wisconsin
> Package (GCG)?
> (As SeqIO can work on GCG formatted seq files as I know.)
> I did not find the possible choices for the " '-format' => " in the
> SearchIO documentation, although it ought to be a list of certain
> exact strings (like "blast" or "fasta" or whatever) that the
> whichever underlying module will try to match/parse when I call
>
> SearchIO -> new ...
>
> I reckon. If I just write:
>
>  '-format' => 'blast'
>
> would it figure out whether the file is from blastall or WU-Blast or
> GCG-Blast or perhaps an HTML output downloaded from NCBI?
>
> Or what can I do with a GCG-Blast output?
>
> thanx
> Peter
> ..................................................................
> ..........
> Peter B. Kos, Ph.D.
> Molecular Microbiology and Genetics Lab.
> Research Institute of Innovative Technology for the Earth (RITE)
> 9-2 Kizugawadai, Kizu-cho, Soraku-gun,
> Kyoto 619-0292 JAPAN
> Phone: +81-774-75-2308
> Fax: +81-774-75-2321
> E-mail: kos@rite.or.jp
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu