[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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