Hi Syed,
FYI, just to clarify using direct Web Services (without going through the 0.7
BioMart Perl API's) seems to work. For example, using the XML file below as a
POST request. If you know of any serious bugs crossing db boundries with this
approach please let me know. Thank you for your help!!
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" formatter = "FASTA" header = "0"
uniqueRows = "1" count = "" datasetConfigVersion = "0.6" >
<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
<Filter name = "with_protein_id" excluded = "0"/>
<Filter name = "chromosome_name" value = "1"/>
<Attribute name = "ensembl_gene_id" />
<Attribute name = "ensembl_transcript_id" />
<Attribute name = "chromosome_name" />
<Attribute name = "strand" />
<Attribute name = "external_gene_id" />
<Attribute name = "5utr" />
</Dataset>
</Query>
________________________________
From: Syed Haider <[email protected]>
To: pip pipster <[email protected]>
Cc: "[email protected]" <[email protected]>
Sent: Thursday, December 29, 2011 10:24 AM
Subject: Re: [BioMart Users] problem with getting sequence data
Hi Phillipe,
Web services are certainly the way to go forward except the current
(v0.7) queries that span genomic sequences such as your request. These
sequences seem to have a bug which is triggered only through the
webservices. The v0.8 does not have the perl API, but an equivalent in
Java, which is essentially identical to its webservice equivalent.
Best,
Syed
On 29/12/2011 02:02, pip pipster wrote:
> Hi Syed,
> Thanks for the suggestion. I had to wait until the evening to try your
> suggestion because my University's firewall apparently block the 53xx ports.
> The results look more pormising using DBLocation. Also, when using Web
> Services (instead of the BioMart Perl API), I seem to get the correct results
> though I still have more testing to do. Would you expect Web Services to be
> the more reliable mechanism when it comes to data integrity issues such as
> this? I wonder if this is one of many reasons why Biomart 0.8 may drop
> support (is that true?) for the BioMart PERL API's.
>
> Do you know why changing the Mart type to MartDBLocation works better than
> MartURLLocation? Given the firewall issues I may have no choice but to
> switch to using the Web Services method.
>
> Thank you,
> Phillipe
>
> ________________________________
> From: Syed Haider<[email protected]>
> To: pip pipster<[email protected]>
> Cc: "[email protected]"<[email protected]>
> Sent: Wednesday, December 28, 2011 1:14 PM
> Subject: Re: [BioMart Users] problem with getting sequence data
>
> Hi,
>
> what happens when you use the MartDBLocation type connection params in
> registry file, e.g:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
>
> <MartDBLocation databaseType="mysql"
> host="martdb.ensembl.org<http://martdb.ensembl.org>"
> database="ensembl_mart_65" name="ensembl" displayName="ENSEMBL 65 GENE
> (SANGER UK)" port="5316" schema="ensembl_mart_65" user="anonymous"
> password="" visible="1" default="1" martUser=""
> includeDatasets="hsapiens_gene_ensembl" />
>
> <MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
> database="sequence_mart_65" name="seq" displayName="ENSEMBL 65 SEQ (SANGER
> UK)" port="5316" schema="sequence_mart_65" user="anonymous" password=""
> visible="1" default="1" martUser="" includeDatasets="" />
>
> </MartRegistry>
>
>
>
> Syed
>
>
>
>
>
>
>
> On 27/12/2011 21:49, pip pipster wrote:
>> <?xml version="1.0" encoding="UTF-8"?>
>> <!DOCTYPE MartRegistry>
>> <MartRegistry>
>> <MartURLLocation database="ensembl_mart_65" default="1"
>>displayName="Ensembl Genes 65" host="www.ensembl.org<http://www.ensembl.org>"
>>includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL"
>>path="/biomart/martservice" port="80" serverVirtualSchema="default"
>>visible="1" />
>> <MartURLLocation database="sequence_mart_65" default=""
>>displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser=""
>>name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80"
>>serverVirtualSchema="default" visible="" />
>> </MartRegistry>
>
>
>
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