[Bioperl-l] SearchIO error

[Jason Stajich]

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