Re: [GUSDEV] Reply for LoadTaxonomy issue

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

Sorry, I read two messages and replied to the wrong one. Obviously this reply
concerns the LoadTaxonomy plugin problem.




Quoting 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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>>
>>
>>
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>>
>>
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>
>
>
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
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