[Bioperl-l] Broken RemoteBlast fixes

[Jason Stajich]

I think I have answered this query at least 5 times privately as well  
as there has been list traffic about it.  We'll need to post a news  
item about it and/or add this to the FAQ.


Everything has been updated to work with the latest NCBI changes -  
you can get working code from Bioperl CVS.  It requires SearchIO/ 
blast.pm patch and RemoteBlast.pm fix.

Bioperl 1.5.1 (RC 1 is up, I just posted about it) will be released  
soon and has these fixes incorporated.

There may well still be problems with the resulting text file that  
NCBI sends back in the future -- they say there is no guarantee that  
it will always be parseable.  The solution is you can always revert  
to the XML output from them and the blastxml SearchIO parser to get  
this data.  Please see my mailing list post from last week about how  
to request the XML format from them.

-jason
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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>

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