Re: [GUSDEV] Blast Similarities

[Mark S. H. <mh...@ug...>]

Hi Adhemar,

See comments inline...

On Jul 11, 2006, at 12:50 PM, Adhemar Zerlotini Neto wrote:

> I'm trying to upload some blast results following a manual created  
> by Pablo, from Jessica's Lab. at UGA.
>
> The problem is that the perl script  
> 'parseBlastFilesForSimilarity.pl' isn't working.
>
> Here is the error:
>

<extraneous error msg cut>

> Analyzing
> opening
> /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/ 
> SJest.VS.SJcontigs.PARSED
> Can't locate object method "new" via package "Blast::BlastAnal"
> (perhaps you forgot to load "Blast::BlastAnal"?) at
> parseBlastFilesForSimilarity.pl line 81.
>
>

This looks like the same problem as before - the script is looking  
for 'Blast::BlastAnal ' but the correct package name is  
CBIL::Bio::Blast::BlastAnal.

> I would like to know how to fix this script or to download a new  
> version of the blast parse scripts.
>

We use the DJob framework for our blast execution and result parsing.  
https://cbil.upenn.edu/svn/gus/DJob/trunk/DistribJob/doc/DistribJob.html

Within the DJob project is a blastSimilarity script. Your  
parseBlastFilesForSimilarity.pl script appears to be pretty much the  
same as DJob's blastSimilarity except blastSimilarity also executes  
the blast command in addition to parsing the result. I don't know of  
any other supported blast parsing script.

The output of blastSimilarity can be loaded into GUS with  
GUS::Supported::Plugin::InsertBlastSimilarities. I believe that's the  
same for your parseBlastFilesForSimilarity.pl

DJob is well documented and a very useful system if you use a compute  
cluster or have several types  of analyses that you want to wrap in a  
pipeline. If you are running your blast on a single machine and just  
want to parse the results for loading into GUS then you will probably  
want to continue to use the parseBlastFilesForSimilarity script.

In summary, fix the package name in your script and continue to use  
that. Email Pablo or me directly if you continue to have problems  
with parseBlastFilesForSimilarity.

-Mark