Re: [GUSDEV] Blast Similarities

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

On Jul 12, 2006, at 12:28 PM, Pablo Mendes wrote:

>
> Hi Adhemar,
> it seems you need the BlastAnal.pm package
>
> > Can't locate object method "new" via package  
> "Blast::BlastAnal" (perhaps you forgot to
> > load "Blast::BlastAnal"?) at
> It is available in a CBIL tar:
> http://www.cbil.upenn.edu/downloads/CBIL/releases/
>
> CBIL/Bio/lib/perl/Blast/BlastAnal.pm
> You might want to change/add a "use lib" to  
> 'parseBlastFilesForSimilarity.pl' or to add the CBIL to your  
> "classpath", changing the $PERL5LIB variable.
> (http://www.perl.com/doc/manual/html/pod/perlrun.html)
>

Add CBIL to your lib path as Pablo says. Also you probably need to  
change the line 'use Blast::BlastAnal;' in  
parseBlastFilesForSimilarity.pl to 'use CBIL::Bio::Blast::BlastAnal;'

(Steve, I don't know the specific origin of  
parseBlastFilesForSimilarity.pl, it's pretty old and no longer (if it  
ever was) a supported GUS script. It is more or less functionally  
equivalent and maybe an ancestor to DJob's blastSimilarity script.)

>
> Good luck,
> Pablo
> ----- Original Message -----
> From: Adhemar Zerlotini Neto
> To: gus...@li...
> Sent: Wednesday, July 12, 2006 11:31 AM
> Subject: [GUSDEV] Blast Similarities
>
> I'm trying to upload some blast results following a manual created  
> by Pablo, who works at Jessica's Lab. at UGA.
>
> The problem is that the perl script  
> 'parseBlastFilesForSimilarity.pl' isn't working.
>
> Here is the error:
>
> perl parseBlastFilesForSimilarity.pl --regex='(\S+)'
> --outputFile=/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/ 
> SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED --dir=/home/japonicum/ 
> JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/ 
> SJest.VS.SJcontigs.RESULTS Opening
> /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/ 
> SJest.VS.SJcontigs.PARSED /home/japonicum/JaponicumDB/PROJECTS_INFO/ 
> BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED is open
> Cutoff parameters:
> P value: 1e-05
> Length: 10
> Percent Identity: 20
>
>
> 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.
>
>
> I would like to know how to fix this script or to download a new  
> version of the blast parse scripts.
>
> Thanks,
>
> Ad.
>
>
>
>
>
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