[Bioperl-l] RemoteBlast not handling NCBI Error message

Chris Fields cjfields at uiuc.edu
Tue Aug 21 12:15:36 EDT 2007


On Aug 21, 2007, at 10:20 AM, Jason Walker wrote:

> I've noticed RemoteBlast does not handle a specific error message from
> NCBI correctly.  retrieve_blast() should return 0 if waiting, -1 on
> error, or the results when completed.  It looks like the method relies
> on a specific tag in the NCBI return,  'QBlastInfoBegin'.  The error
> message I'm getting does not have this tag or a value of
> 'Status=ERROR'.  After contacting NCBI 'Blast-help', they stated that
> QBlastInfoBegin should not be expected from all GET requests.  The  
> error
> can be reproduced by using RID CM2YJJW501R, until it expires tomorrow.
> ...
> I added a conditional statement as seen below to correct my local  
> copy.
> I'm not sure this is the best fix, but it works.
> sub retrieve_blast {
>     ...
>     if( /QBlastInfoBegin/i ) {
>         $s = 1;
>     } elsif( $s ) {
>         if( /Status=(WAITING|ERROR|READY)/i ) {
>             ...
>          }
>     } elsif( /^(?:#\s)?[\w-]*?BLAST\w+/ ) {
>         $waiting = 0;
>         last;
>     } elsif ( /ERROR/i ) {
>         close($TMP);
>         open(my $ERR, "<$tempfile") or $self->throw("cannot open file
> $tempfile");
>         $self->warn(join("", <$ERR>));
>         close $ERR;
>         return -1;
>     }
>     ...
> }
>
> Thanks,
> Jason Walker

I have added this to RemoteBlast in bioperl cvs.  Thanks for the notice!

chris


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