[Bioperl-l] RE: SearchIO and GCG

[Peter Kos]

Hi,

thanks for the concern.
I will try to go through those files.
I must admit that again I just circumvented my problem rather then 
really solving it straight.
I knew, I the databases shipped with gcg are in special format. Which 
is true for the annotated databases like gb, embl, pir and stuff like 
that. However, as I figured out that "blast" (in gcg) is just a 
wrapper for "blastall v.2" and the corresponding databases are in 
exact NCBI blast format. Therefore, instead of working on some 
solution of the possible minor differences, I simply disregarded that 
annoying wrapper and used the good old  blastall with the gcg 
databases.
I am sorry that I asked you before careful examination of the case, 
causing extra work on your side.

Can I find that  t/data/test.gcgblast on a public place? I bet you 
keep this kind of new things on a server but I am not aware of that 
exact location.

Sorry for the inconvenience and thanx for the help, any way.
Peter

On Friday, August 09, 2002 1:01 PM, Jason Stajich 
[SMTP:jason@cgt.mc.duke.edu] wrote:
> 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



..................................................................  
..........
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