[Bioperl-l] StandAloneBlast & SeqIO very strange stream

[Jason Stajich]

Any reason you don't just blast it all in one go with
% blastall -i filename -o output -p blastp
This will be faster than doing them individually.

If you still want them in separate files just write a simple script
which splits on /^BLASTP/ ?

No idea why you're getting the described behavior below except that the
blast running module may be cleaning up outputfiles so you're just seeing
things in progress.

-jason

On Mon, 17 Mar 2003, Remo Sanges wrote:

> If I want to save a blast.out file for every sequence in a flat file
> with this sintax:
>
> $str = Bio::SeqIO->new(-file=>'sequences' , '-format' => 'fasta' );
> while ($input = $str->next_seq())	{
> 	my @params=(	'p'=>$ARGV[2],
> 			'd'=>"$singledb",
> 			'o'=>"$string",
> 			'e'=>$ARGV[3]	);
> 	$blast_report = $factory->blastall($input);
> 	}
>
> the blast_report is created and it is possible to parse it with
> Bio::SearchIO, but the stream save only the 50% of outfile (the 2th,
> 4th, 6th, 8th..........sequence in the flatfile).
>
> This appens with bioperl-1.0, bioperl-1.2, bioperl-1.2.1-rc1
>
> Why?
> How can I save a blast.out file for every sequence?
>
> Thanks
>
> Remo Sanges
> BioGeM - IGB
> Naples
>
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>

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