Re: [GUSDEV] Blast Similarities

[<pi...@pc...>]

One possibility:

You might not be in the right group or group write is not set properly on the
child table. If true, the plugin is not able to update the child row's 
taxon_id
and therefore deleting that taxon row would violate a foreign key constraint.
Check the core.groupinfo for which group you're in and the group_write 
field in
the child table.

Debbie




Quoting Pablo Mendes <pa...@ug...>:

>
> 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)
>
>
> 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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