[Bioperl-l] SearchIO error

[Jason Stajich]

On Wed, 30 Jun 2004, michael watson (IAH-C) wrote:

> Ooops, I was using it incorrectly - RTFM etc :-)
>
> Having said that though, for consistency, if one has to pass a writer
> object to SearchIO, shouldn't one also have to pass a writer to SeqIO?
> Presumably when one specifies (-format=>EMBL, -file=>">out.embl") in
> SeqIO, then internally bioperl goes to get an EMBL writer object anyway?
> So maybe the internals of SeqIO and SearchIO are pretty similar, yet in
> one you pass a -format argument, and in another you pass a writer
> object.

Not really.  We didn't decide to do it that way for SearchIO.  There
internals for autoloading a format module is similar but not identical.
At first I never intended the writers to be plugged into SearchIO - you
just call my $string = $writer->to_string($result);

and SearchIO plugging was added later and so it seems a little hacky.  I
don't really want to mess with it now.

>
> Though I could, of course, be completely wrong.
>
> Thanks for the help!
>
> Mick
>
> -----Original Message-----
> From: Jason Stajich [mailto:jason at cgt.duhs.duke.edu]
> Sent: 23 June 2004 14:17
> To: michael watson (IAH-C)
> Cc: Bioperl-l
> Subject: Re: [Bioperl-l] SearchIO error
>
>
> More correctly - what do you want to see in your out.blast?  a table?
> the blast report?
>
> If you read the docs for how to use a hit writer you'll see it isn't as
> parallel to SeqIO type ways - you need to give SearchIO a writer object
> when you initialize it for writing.  But if you are just re-writing out
> a blast file why parse it with SearchIO in the first place?
>
> -jason
>
> On Wed, 23 Jun 2004, michael watson (IAH-C) wrote:
>
> > Hi
> >
> > I am using bioperl-1.4 now.  I seem to get an error when using
> > SearchIO. Perhaps I am not using it correctly?  My script is:
> >
> > my $fh = new IO::File;
> > $fh->open("/usr/bin/blastall -p blastp -i test.fasta -d 10287/set2
> > |");
> >
> > my $searchio = Bio::SearchIO->new(-format => 'blast', -fh => $fh); my
> > $result = $searchio->next_result;
> >
> > my $search_out = Bio::SearchIO->new(-format => 'blast', -file =>
> > ">test_out.blast"); $search_out->write_result($result);
> >
> > $fh->close;
> >
> > The error I get is:
> >
> > -------------------- WARNING ---------------------
> > MSG: Writer not defined. Using a Bio::Search::Writer::HitTableWriter
> > ---------------------------------------------------
> > Can't locate object method "new" via package
> > "Bio::Search::Writer::HitTableWriter" (perhaps you forgot to load
> > "Bio::Search::Writer::HitTableWriter"?) at
> > /usr/local/bioperl-1.4/Bio/SearchIO/blast.pm line 1493, <GEN0> line
> > 397.
> >
> > Can anyone be of help?
> >
> > Thanks
> > Mick
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>

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