[Bioperl-l] RemoteBlast save_output does not handle -m8 output correctly

[Jason Stajich]

You'll need to fix this logic which expects to see a BLAST HEADER  
before it starts writing.  If someone post a patch we can apply the fix.

    while(my $l = <TMP>) {
                 next if ($l =~ /<pre>/);
                 if( $l =~ /^(?:[T]?BLAST[NPX])\s*.+$/i ||
                          $l =~/^RPS-BLAST\s*.+$/i ) {
                         $seentop=1;
                 }
                 next if !$seentop;
                 if( $seentop ) {
                         print SAVEOUT $l;
                 }
         }

On Sep 1, 2005, at 2:58 PM, Paul G Cantalupo wrote:

> Hello,
>
> I'm using bioperl-1.4 and I noticed that RemoteBlast save_output  
> method creates an empty file (zero bytes) when dealing with blast - 
> m8 output (i.e. ALIGNMENT_VIEW = Tabular). Is there a fix for this?
>
> Thank you,
>
> Paul
>
> Paul Cantalupo
> Research Specialist/Systems Programmer
> 559 Crawford Hall
> Department of Biological Sciences
> University of Pittsburgh
> Pittsburgh, PA 15260
> Work: 412-624-4687
> Fax: 412-624-4759
>
> Ask me about Toastmasters: www.toastmasters.org
> Midday Club Treasurer
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12