[Bioperl-l] net blast not accommodated to the current NCBI?

[Jason Stajich]

Don't use this Bio::Tools::Blast for this anymore.

See Bio::Tools::Run::RemoteBlast for remote blast.

On Thu, 14 Mar 2002, Guoneng Zhong wrote:

> Hi,
>
> I am trying to send a remote Blast search and I get this error:
>
> -------------------- EXCEPTION --------------------
> MSG: Blast file tigre0og69F8_1.tblastx2.nr.temp.html is incomplete:
> can't find program name.
> Possibly an unrecognized report format.
>
> I looked at the html in question and it is the page you get on NCBI
> while you are waiting for the blast to complete.  When you submit a
> search on NCBI you don't get the search result immediately, but this "Be
> Patient" page.  After a few minutes you can click on the Format button
> and hope to get the result.  I was expecting the Blast.pm class to be
> doing that, waiting and waiting till it's ready.  Maybe I gave it the
> wrong param?  Here's my simple code:
>
> use Bio::SeqIO;
>
> my $format = "Fasta";
> my $filename = $ARGV[0] || die "Need to know what file!";
> my $sequence = Bio::SeqIO->new
> (-file=>$filename,-format=>$format)->next_primary_
> seq;
> my @sequences = ($sequence);
> my %runParams = (
>          -method=>'remote',
>          -prog=>'tblastx',
>          -version=>2,
>          -html=>0,
>          -seqs=>[$sequence]
>          );
> my $blastObj = Bio::Tools::Blast->new(
>                  -run => \%runParams,
>                  -file=>'test.out',
>                  -parse => 1,
>                  -signif =>'1e-10',
>                  -strict =>1
>                  );
>
>
> Thanks in advance for any help!
>
> Oh, yes, I am aware of the example for remote blast, but reading it
> discouraged me from not writing my own blast search....
>
I don't understand what you mean.  which example.  what discouraged you?
You're using old code that has not been maintained.
You're welcome to write your own if you think you can provide a
better interface, let us know and we can consider adding it to the
toolkit.

> G
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

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