[ensembl-dev] BioMart Ensembl version
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Wed Sep 24 12:13:26 BST 2014
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>
>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>> 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
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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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>>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
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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/
>
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
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> Ensembl Blog: http://www.ensembl.info/
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