[ensembl-dev] EFG array mappingenvironmentprobe2transcriptfailslooking fortranscript_stable_id table

Oliver, Gavin gavin.oliver at almacgroup.com
Wed Jul 18 11:51:17 BST 2012


Hi Nathan, 

 

I was a bit confused by this as all my database naming variables were
set to the same format as specified in the documentation.  I checked my
mysql databases and saw the following:

 

+---------------------------------------------+

| Database                                    

+---------------------------------------------+

| arrays_pipeline_funcgen_67_37  

| arrays_pipeline_homo_sapiens_funcgen_60_37e 

| arrays_pipeline_homo_sapiens_funcgen_61_37f 

| arrays_pipeline_homo_sapiens_funcgen_67_37  

 

So there was a database in there with the correct naming format and one
with the wrong one.   Perhaps the wrongly named one came about from an
earlier run before variables had been set properly.  Anyway, I dropped
the database and reran the scripts without specifying the
species/port/db version.  They now run ok.  Recreating a database with
the name arrays_pipeline_funcgen_67_37 causes them to fail again.  I am
not sure exactly what route the error comes about by?

 

Although it may not be important now,  the only thing I was changing in
the array_example.pl script was to change

 

$registry->load_registry_from_db

  (

   -host => 'ensembldb.ensembl.org',

   -user => 'anonymous',

  );

 

To

 

$registry->load_registry_from_db

  (

   -host => 'ni-ca-svc-bs3',

   -user => 'goliver',

   -pass=>'pass'

  );

 

And the entire error output was as I sent before:

 

arrays:homo_sapiens_funcgen_67_37>perl array_example.pl

:: Failed to find dnadb like arrays_pipeline_core_%_37%, using
anonymous at ensembldb.ensembl.org:5306 at
/cluster_progs/data/Ensembl/67/ensembl-functgenomics/modules//Bio/EnsEMB
L/Funcgen/DBSQL/DBAdaptor.pm line 608.

 

 

 

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf
Of Nathan Johnson
Sent: 18 July 2012 10:30
To: Ensembl developers list
Subject: Re: [ensembl-dev] EFG array
mappingenvironmentprobe2transcriptfailslooking fortranscript_stable_id
table

 

Hi Gavin

 

I'm a little confused about exactly how this error was generated. If you
ran the array_example.pl script how did it know about your DB? Can you
give me the full stack trace from the array_example.pl script, and your
edited code with parameter values?

 

The error you are seeing below is due to one of the functions of the
funcgen DBAdaptor, if no dnadb is specified it tries to automatically
select the correct one based on the species and the dbname of the
funcgen DB you are using i.e. matching the species and assembly version.
It appears to this the species is 'arrays_pipeline'.  Incidentally, the
array mapping pipeline requires a standard DB naming convention which is
detailed in the array mappings docs:

 

your_prefix_species_name_funcgen_RELEASE_BUILDversion 

e.g. my_homo_sapiens_funcgen_54_37p

 

Altho we have since dropped the version letter at the end, so I will
update this. You should really correct this, but admittedly this is not
the root cause of the problem here.

 

Nath

 

 

On 18 Jul 2012, at 10:11, Oliver, Gavin wrote:





Hi Nathan,

 

Error output is as follows:

 

:: Failed to find dnadb like arrays_pipeline_core_%_37%, using
anonymous at ensembldb.ensembl.org:5306 at
/cluster_progs/data/Ensembl/67/ensembl-functgenomics/modules//Bio/EnsEMB
L/Funcgen/DBSQL/DBAdaptor.pm line 608.

 

I just reconfirmed (and re-reconfirmed) that removal of the species
definition will cause this error to be thrown.

 

Best,

 

Gavin

 

 

 

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf
Of Nathan Johnson
Sent: 18 July 2012 09:43
To: Ensembl developers list
Subject: Re: [ensembl-dev] EFG array mapping
environmentprobe2transcriptfailslooking for transcript_stable_id table

 

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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Dev mailing list    Dev at ensembl.org
List admin (including subscribe/unsubscribe):
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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

 

 













 

_______________________________________________
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

 

 













 

_______________________________________________
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

 

 











 

_______________________________________________
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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