[Bioperl-l] Re: SearchIO and GCG

[Peter Kos]

Thank you, Jason.

I see.
So it means, that either I write a small filter converting the 
headers to NCBI format, or try to understand/learn/figure out how 
these files are read in and parsed by the Bioperl modules and alter 
that.
Or forget about GCG altogether.

Hmm. The first one seems completely silly, a bit uncomfortable to 
use, but perhaps easy to do.
The second one seems really cool, appropriate and elegant, but quite 
a tough challenge (to be modest).
As for the third one, it would be a shame abusing the Internet and 
NCBI throughput, when I have here the package with the GCG-formatted 
databases.

I'll think about it. Thank you anyway.

Best regards
Peter

On Friday, July 26, 2002 9:49 PM, Jason Stajich 
[SMTP:jason@cgt.mc.duke.edu] wrote:
> Subtle differences for what I can tell - should be possible with a
> few
> tweaks to blast.pm.  It is not different enough to warrant a
> Bio::SearchIO
> driver since it is just a clone of NCBI blast with different
> headers.
>
> -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
> > ..............................................................  
....
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
..................................................................  
..........
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