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

[Guoneng Zhong]

Well, I don't have that module named RemoteBlast in my bioperl.  Am I 
supposed to?  It's not in the bioperl online docs.  I thought maybe it 
is Webblast, but it gave the exact same error as last time.  
Incidentally, Blast.pm uses Webblast.

G

On Thursday, March 14, 2002, at 01:26 PM, Jason Stajich wrote:

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