[ensembl-dev] EFG array mapping environment probe2transcriptfailslooking for transcript_stable_id table

Nathan Johnson njohnson at ebi.ac.uk
Wed Jul 18 09:43:16 BST 2012


Can you send me the error output please? I can't diagnose the problem without knowing how it was failing.

I doubt you have to specify -species to the load method as this simply restricts what is loaded. The fact you have to specify -db_version makes me think you are possibly running with the HEAD code which is version 68, against a sever which has no version 68 DBs (as we have not released them yet), hence by default it won't load anything unless you specify a -db_verison to match your DBs.


Nath


On 18 Jul 2012, at 09:34, Oliver, Gavin wrote:

> Hi Nathan,
>  
> I found a way around the problem.
>  
> Originally  the script worked like this:
>  
> my $registry = "Bio::EnsEMBL::Registry";
> $registry->load_registry_from_db(
> -host => $host,
> -user => $user,
> -pass => $pass,
> -db_version => $version,
>                         );
>  
> my $aa            = $registry->get_adaptor("homo sapiens","funcgen","Array");
> my $array = $aa->fetch_by_name_vendor($array_id, 'AFFY');
>  
> Now I have to also specify –port, -species and –db_version in the call to the load_registry_from_db method (originally these were defined elsewhere in the efg environment), otherwise the Funcgen::DBSQL::DBAdaptor module reverts to default database settings.
>  
>  
> Best,
>  
> Gavin
>  
>  
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Nathan Johnson
> Sent: 17 July 2012 11:40
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] EFG array mapping environment probe2transcriptfailslooking for transcript_stable_id table
>  
> Also, can you send me the output of the array_example.pl script?
>  
> Thanks
>  
> Nath
> On 17 Jul 2012, at 11:36, Nathan Johnson wrote:
> 
> 
> Hi Gavin
>  
> Did you run the array_example.pl script 'as is', or did you make any changes?
>  
>  
> Nath
>  
> On 16 Jul 2012, at 15:21, Oliver, Gavin wrote:
> 
> 
> Thanks Nathan, that seemed to work however I immediately hit an issue when I try to connect to the database to utilise the data.
>  
> The problem seems to be with getting the array adaptor – the Funcgen::DBSQL::DBAdaptor module keeps reverting to default database settings.  It looks like the problem occurs here:
>  
> my ( $dnadb_host, $dnadb_user, $dnadb_port, $dnadb_pass, $dnadb_assm, $dnadb_name, $dnadb)
>     = rearrange( [ 'DNADB_HOST', 'DNADB_USER',
>                  'DNADB_PORT', 'DNADB_PASS',
>                                   'DNADB_ASSEMBLY', 'DNADB_NAME',
>                                   'DNADB'
>                 ],
>                 @args );
>  
> The @args array is populated but the rearrange method doesn’t seem to work on it.
>  
> The error occurs when I run my my scripts but I have also reproduced it using the array_example.pl script included with the API.
>  
>  
>  
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Nathan Johnson
> Sent: 11 July 2012 16:55
> To: Ensembl developers list
> Subject: [ensembl-dev] EFG array mapping environment probe2transcript failslooking for transcript_stable_id table
>  
> Hi Gavin
>  
> Please be patient when using the dev list and always keep the conversation on the list, un-invited off list contact is unacceptable (see posting guidelines attached).
>  
> wrt the error you have found, it seems that this fix has been hanging around in my local repository for a while and missed check in for some reason.  I have now checked in the updated methods on the head. You can try checking out the head code and simply copying the Helper.pm to your v67 checkout. 
>  
> Thanks
>  
> Nathan Johnson
> Senior Scientific Programmer
> Ensembl Regulation
> European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
>  
> http://www.ensembl.info/
> http://twitter.com/#!/ensembl
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> On 11 Jul 2012, at 10:53, Oliver, Gavin wrote:
> 
> 
> 
> Hi Nathan,
> 
> Sorry to contact you directly but I am not having much luck on the mailing list.
>  
> I am leaving Almac in a couple of weeks (off to the Mayo Clinic) and have been asked to update our array annotations before I go.  I have not updated the annotations/APIs etc since v60 and am now trying to update to v67.
>  
> I have got as far as the RunTranscriptXrefs stage but then it is failing when the Helper.pm module looks for the transcript_stable_id table which appears to have been removed from the core schema after v64.
>  
> Are there any known issues with the current API version?
>  
> Best,
>  
> Gavin
>  
>  
>  
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>  
> Nathan Johnson
> Senior Scientific Programmer
> Ensembl Regulation
> European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
>  
> http://www.ensembl.info/
> http://twitter.com/#!/ensembl
>  
>  
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> 
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> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>  
> Nathan Johnson
> Senior Scientific Programmer
> Ensembl Regulation
> European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
>  
> http://www.ensembl.info/
> http://twitter.com/#!/ensembl
>  
>  
> 
> 
> 
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Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

http://www.ensembl.info/
http://twitter.com/#!/ensembl






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