Re: blastall problem

hi Torsten,
Yes, it still gives me the same error even if I give the full path to the fasta file. Following is how I did:

####### part of my script #######
my $Seq_in = Bio::SeqIO->new (-file => '/export/home/local/apache2/htdocs/result/fasta.faa', -format => 'Fasta');
my $queryin = $Seq_in->next_seq();
my $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => 'blastp',
                                                 'database' => '/export/home/dorjee/database/nrpart',
                                                 _READMETHOD => 'Blast'
                                                   );
$factory->outfile("/export/home/local/apache2/htdocs/result/out.blast");
my $blastreport = $factory->blastall($queryin);
....

thanks man.

Torsten Seemann wrote:

> Software error:
> ------------- EXCEPTION  -------------
> MSG:    not Bio::Seq object or array of Bio::Seq objects or file name!
> STACK Bio::Tools::Run::StandAloneBlast::blastpgp
> /usr/perl5/5.6.1/lib/Bio/Tools/Run/StandAloneBlast.pm:611
> STACK toplevel /usr/local/apache2/htdocs/remote_ncbi.pl:50

> my $Seq_in = Bio::SeqIO->new (-file => 'result/fasta.faa', '-format' => 'Fasta');

Does this still happen if you give the full path to the FASTA file?
eg. -file => /usr/local/apache2/htdocs/result/fasta.faa
(I'm guessing what the full path is here)

--Torsten
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