[Bioperl-l] Broken RemoteBlast fixes

[Aaron J. Mackey]

Nitpicky point:

   /:{0,1}/ is equivalent to (and overkill for) /:?/

-Aaron

On Sep 22, 2005, at 11:02 AM, Leo, Paul (NIH/NHGRI) wrote:

> So I come back from a "bio-perl break" and my code is spitting the  
> dummy.
>
>
>
> RemoteBlast was DOA.
>
>
>
> I see there is some discussion about this in Septembers mailing list
> archives; the fixes that worked for me were changing:
>
> Scott Markel : ( $size > 1000 ) to ( $size > 2000 ) in RemoteBlast.pm
>
> AND
>
> paul.boutros : line 1145 of Bio\SearchIO\blast.pm this way:
> -1145:        if( /^((Query|Sbjct):\s+(\-?\d+)\s*)(\S+)\s+(\-?\d 
> +)/ ) {
> +1145:        if( /^((Query|Sbjct):{0,1}\s+(\-?\d+)\s*)(\S+)\s+(\-? 
> \d+)/ ) {
>
> I had to make BOTH changes for it to work.
>
> Note that BioPerl 1.4 form ActiveState does not have these changes  
> and does
> not work which I'm sure will confuse the hell out of any new users!
>
>
> Question: are these the best fixes to use, are these modules  
> working in 1.5?
>
>
>
> Thanks
>
> Paul
>
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--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  amackey at pcbi.upenn.edu
office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
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