[Bioperl-l] Warning while running bioperl StandAloneBlast.

[shalabh sharma]

Hi Praveen,
                 Your script is bit confusing, i don't understand what you
actually trying to do.
But what i see is that you are parsing blast report without using SearchIO
module.
You have to include Bio::SearchIO in your script.
Hope this helps.

-Shalabh Sharma

On Tue, May 19, 2009 at 8:03 AM, Praveen Surendran <
praveen_spillai at yahoo.co.in> wrote:

> Hi,
>
> I am getting some warning along with results which says --> "[NULL_CAPTION]
> Warning: Failed to initialize search. ISAM Error code is -5"
> Can someone please let me know what this is all about.
>
> Please find my script below.
>
>
> ----------------------------------------------------------------------------------
> use Bio::SeqIO;
> use Bio::Tools::Run::StandAloneBlast;
> open FILE, ">./blast.txt";
> my $Seq_in = Bio::SeqIO->new (-file => $ARGV[0],
>                                -format => 'fasta');
> my $query = $Seq_in->next_seq();
> my $factory = Bio::Tools::Run::StandAloneBlast->new( 'program'  =>
> 'blastn',
>     'database' => 'nr',
>     _READMETHOD => "Blast" );
> my $blast_report = $factory->blastall($query);
> my $result = $blast_report->next_result;
> while( my $hit = $result->next_hit()) {
>   print FILE "\thit name: ", $hit->name(), " significance: ",
> $hit->significance(), "\n";
>   # while( my $hsp = $hit->next_hsp()) {
>   # print "E: ", $hsp->evalue(), "frac_identical: ",
> $hsp->frac_identical(), "\n";    }}
> }
>   close FILE
>
> -----------------------------------------------------------------------------------
>
> Kind Regards,
>
> Praveen Surendran.
>
>
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