[ensembl-dev] BioMart Ensembl version
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Wed Sep 24 12:20:45 BST 2014
Sorry forgot to paste error:
Processing Cached Registry:
/share/apps/local/biomart-perl/conf/cachedRegistries/martURLLocation_ensembl_76_hg38.xml.cached
Attribute 'external_gene_id' not found in dataset
default.hsapiens_gene_ensembl
Trace begun at /share/apps/local/biomart-perl/lib/BioMart/Registry.pm
line 490
BioMart::Registry::getAttribute('BioMart::Registry=HASH(0x12746720)',
'hsapiens_gene_ensembl', 'external_gene_id', 'default', 'default')
called at /share/apps/local/biomart-perl/lib/BioMart/Query.pm line 1243
BioMart::Query::addAttribute('BioMart::Query=HASH(0x2af76807f600)',
'external_gene_id') called at local.pl line 892
I've tried with both Biomart 0.6 and 0,7 versions without luck on
Ensembl 76.
On 24/09/14 13:13, Guillermo Marco Puche wrote:
> Dear Thomas,
>
> I'm experiencing an error when querying to BioMart Ensembl 76 registry
> for both clean/cached.
> Using older Mart Registry to ensembl 75 registry archive works for
> both clean/cached.
>
> my $action='clean';
>
> my $initializer =
> BioMart::Initializer->new('registryFile'=>$confFile,
> 'action'=>$action);
> my $registry = $initializer->getRegistry;
>
> my $query =
> BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');
>
> $query->setDataset("hsapiens_gene_ensembl");
> if ( length($gene_name)==15 && substr($gene_name,0,4)
> eq "ENSG" ) { $query->addFilter("ensembl_gene_id", @{$gene}); }
> else { $query->addFilter("hgnc_symbol", @{$gene}); }
> if ($query_type eq "gene_info"){
> #$query->addFilter("biotype", ["protein_coding"]);
> $query->addAttribute("ensembl_gene_id");
> $query->addAttribute("ensembl_transcript_id");
> $query->addAttribute("chromosome_name");
> *$query->addAttribute("external_gene_id");*
> }
>
> Was this removed in Ensembl 76? Is there any documentation about
> BioMart available queries per Ensembl release?
>
> Thank you and sorry for spam, I never had this issues when changing
> Ensembl previously.
>
> Best regards,
> Guillermo.
>
>
> On 23/09/14 15:10, Guillermo Marco Puche wrote:
>> Dear Thomas,
>>
>> Ok I didn't understand correctly, now I do.
>> As you say biomart website registry is still showing ensembl 75.
>>
>> Thank you.
>>
>> Best regards,
>> Guillermo.
>>
>> On 23/09/14 14:01, Thomas Maurel wrote:
>>> Dear Guillermo,
>>>
>>> The biomart.org <http://biomart.org> website seems to be very slow
>>> at the moment and I am afraid the website is still displaying our
>>> release 75 marts on hg19 (GRCh37). According to the biomart.org
>>> <http://biomart.org> mart registry page:
>>> http://www.biomart.org/biomart/martservice?type=registry, port '80'
>>> is still valid.
>>> If you want to use hg38 (GRCh38), the best way would be to point
>>> your mart XML config to the ensembl.org <http://ensembl.org> website
>>> in order to access our release 76 mart databases on hg38 (GRCh38).
>>> You can follow the previous instruction but just change the mart
>>> registry URL page to get the mart release 76 registry informations:
>>>
>>>>> 2) A BioMart perl script
>>>>> a) You first need to edit your configuration file in
>>>>> "biomart-perl/conf/martURLLocation.xml" and paste the content of
>>>>> the mart registry page for the
>>> Ensembl website on release 76 (hg38):
>>> http://www.ensembl.org/biomart/martservice?type=registry
>>>>> b) Then edit your script and make sure that "my $confFile"
>>>>> variable is looking at the martURLLocation.xml configuration file
>>>>> in biomart-perl/conf
>>>>> c) Finally, make sure to update the following line in your script:
>>>>>
>>>>> my $action='cached';
>>>>>
>>>>> with:
>>>>>
>>>>> my $action='clean';
>>>>>
>>>>> The first run of your script on Ensembl 75 might be a bit slow as
>>>>> BioMart will cache some data from the BioMart website.
>>>>> Once you have run your script with the action variable set to
>>>>> "clean", you can set the variable to "cached" again.
>>>
>>> I am afraid $action=clean is quite resource consuming but you will
>>> only need to run your script with this setting when you change the
>>> registry information.
>>>
>>> Hope this helps,
>>> Best regards,
>>> Thomas
>>> On 23 Sep 2014, at 12:43, Guillermo Marco Puche
>>> <guillermo.marco at sistemasgenomicos.com
>>> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>>
>>>> Dear Thomas,
>>>>
>>>> My BioMart perl script is using the following mart XML config file:
>>>>
>>>> <?xml version="1.0" encoding="UTF-8"?>
>>>> <!DOCTYPE MartRegistry>
>>>> <MartRegistry>
>>>> <MartURLLocation
>>>> name = "ensembl"
>>>> displayName = "ensembl"
>>>> host = "www.biomart.org"
>>>> port = "80"
>>>> visible = "1"
>>>> default = ""
>>>> includeDatasets = "hsapiens_gene_ensembl"
>>>> martUser = ""
>>>> />
>>>> </MartRegistry>
>>>>
>>>> However, I'm getting BioMart queries from hg19 and not hg38. Does
>>>> the default port '80' still working on hg19? how can I specify I
>>>> would like to use hg38 biomart service.
>>>>
>>>> On the other hand, it's always useful to know how to query older
>>>> Ensembl versions with Biomart. However using $action=clean with
>>>> conf file of ensembl 75 archive it's leading me to massive amounts
>>>> of RAM consumption in my Perl script.
>>>>
>>>> Thanks.
>>>>
>>>> Best regards,
>>>> Guillermo.
>>>> On 19/09/14 15:48, Thomas Maurel wrote:
>>>>> Dear Guillermo,
>>>>>
>>>>> If you are using:
>>>>> 1) the biomart-perl/scripts/webExample.pl script and an xml file
>>>>> You can change the path to the biomart website in the following line:
>>>>>
>>>>> my $path="http://www.biomart.org/biomart/martservice?";
>>>>>
>>>>> With the path to our Ensembl release 75 archive:
>>>>>
>>>>> my
>>>>> $path="http://feb2014.archive.ensembl.org/biomart/martservice?";
>>>>>
>>>>>
>>>>> 2) A BioMart perl script
>>>>> a) You first need to edit your configuration file in
>>>>> "biomart-perl/conf/martURLLocation.xml" and paste the content of
>>>>> the mart registry page for the Ensembl release 75 archive website:
>>>>> http://feb2014.archive.ensembl.org/biomart/martservice?type=registry
>>>>> b) Then edit your script and make sure that "my $confFile"
>>>>> variable is looking at the martURLLocation.xml configuration file
>>>>> in biomart-perl/conf
>>>>> c) Finally, make sure to update the following line in your script:
>>>>>
>>>>> my $action='cached';
>>>>>
>>>>> with:
>>>>>
>>>>> my $action='clean';
>>>>>
>>>>> The first run of your script on Ensembl 75 might be a bit slow as
>>>>> BioMart will cache some data from the BioMart website.
>>>>> Once you have run your script with the action variable set to
>>>>> "clean", you can set the variable to "cached" again.
>>>>>
>>>>> Hope this helps,
>>>>> Best regards,
>>>>> Thomas
>>>>> On 19 Sep 2014, at 13:28, Guillermo Marco Puche
>>>>> <guillermo.marco at sistemasgenomicos.com
>>>>> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>>>>
>>>>>> Dear developers,
>>>>>>
>>>>>> I would like to know how to specify BioMart Perl code to query
>>>>>> against older Ensembl version (ie:75) and not latest (I believe
>>>>>> used by default).
>>>>>>
>>>>>> Thank you.
>>>>>>
>>>>>> Best regards,
>>>>>> Guillermo.
>>>>>> _______________________________________________
>>>>>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
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>>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>
>>>>> --
>>>>> Thomas Maurel
>>>>> Bioinformatician - Ensembl Production Team
>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>> European Molecular Biology Laboratory
>>>>> Wellcome Trust Genome Campus
>>>>> Hinxton
>>>>> Cambridge CB10 1SD
>>>>> United Kingdom
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>> Ensembl Blog:http://www.ensembl.info/
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>>>
>>> --
>>> Thomas Maurel
>>> Bioinformatician - Ensembl Production Team
>>> European Bioinformatics Institute (EMBL-EBI)
>>> European Molecular Biology Laboratory
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridge CB10 1SD
>>> United Kingdom
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing listDev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog:http://www.ensembl.info/
>>
>>
>>
>>
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>
>
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