[Bioperl-l] StandAloneBlast & SeqIO very strange stream

Remo Sanges sanges at biogem.it
Mon Mar 17 17:42:42 EST 2003


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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