[Bioc-devel] biomaRt help
Wolfgang Huber
huber at ebi.ac.uk
Tue Jun 16 13:57:22 CEST 2009
Dear Julie,
thanks for reporting this. I have tried your code
library(biomaRt)
mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
seq1 = getSequence(id = "ENSDARG00000054562",
type = "ensembl_gene_id", seqType = "gene_exon_intron",
upstream = 350, mart = mart)
and reproduced the error:
Errore in getBM(c(seqType, type), filters = c(type, "upstream_flank"),:
Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT
FOUND
both on
R 2.9.0 with biomaRt_2.0.0, RCurl_0.98-1, XML_2.5-1
and
R 2.10.0 with biomaRt_2.1.0, RCurl_0.98-1, XML_2.5-1
We will investigate.
Thanks
Wolfgang
Julie Zhu ha scritto:
> Dear Wolfgang,
>
> Thank you very much for trying the code and pointing out the typo!
>
> I just tried the code again three times. The getBM call produced the error
> on the first and third time, but on the second time the getBM call works
> fine. Here is the code I ran and the output including time, date and session
> information.
>
> Best regards,
>
> Julie
>
>> library(biomaRt)
>> mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
> Checking attributes ... ok
> Checking filters ... ok
>> date()
> [1] "Mon Jun 15 08:35:19 2009"
>> seq1 = getSequence(id = "ENSDARG00000054562",
> + type = "ensembl_gene_id", seqType = "gene_exon_intron",
> + upstream = 350, mart = mart)
> Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"), :
> Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT
> FOUND
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] biomaRt_2.0.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 XML_2.3-0
>> library(biomaRt)
>> mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
> Checking attributes ... ok
> Checking filters ... ok
>> date()
> [1] "Mon Jun 15 08:36:09 2009"
>> seq1 = getSequence(id = "ENSDARG00000054562",
> + type = "ensembl_gene_id", seqType = "gene_exon_intron",
> + upstream = 350, mart = mart)
>> date()
> [1] "Mon Jun 15 08:36:39 2009"
>> seq1 = getSequence(id = "ENSDARG00000054562",
> + type = "ensembl_gene_id", seqType = "gene_exon_intron",
> + upstream = 350, mart = mart)
> Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"), :
> Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT
> FOUND
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] biomaRt_2.0.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 XML_2.3-0
>
>
> On 6/14/09 4:00 AM, "Wolfgang Huber" <huber at ebi.ac.uk> wrote:
>
>> Dear Julie
>>
>> I ran the code below and it worked fine for me. If you want help, can
>> you try being more precise than "sometimes produces error but sometimes
>> not" - e.g. exactly specify the sessionInfo() and the code you run in
>> both cases, and the time and date?
>>
>> There could be a multitude of reasons, which we need to exclude step by
>> step, such as your using different versions of R and its packages,
>> different BioMart servers, different types of internet connection. I
>> would not be surprised if your problem were a biomaRt package version issue.
>>
>> Best wishes
>> Wolfgang
>>
>> PS - Your code example contained a typo and could not have worked
>> (uppercase "L" in the "library" function). Please be sure to always
>> report precisely what you're doing and don't assume small details don't
>> matter.
>>
>>
>> library(biomaRt)
>> mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
>> seq1 = getSequence(id = "ENSDARG00000054562",
>> type = "ensembl_gene_id", seqType = "gene_exon_intron",
>> upstream = 350, mart = mart)
>> seq1
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> gene_exon_intron
>> 1 GTGTCTTTTCCCTCCCCTGGGAAATGATCGTATGTCTACAGTCTCCATCT....
>> ensembl_gene_id
>> 1 ENSDARG00000054562
>>
>>> sessionInfo()
>> R version 2.10.0 Under development (unstable) (2009-06-12 r48755)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8
>> [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices datasets utils methods base
>>
>> other attached packages:
>> [1] biomaRt_2.1.0 fortunes_1.3-6
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_0.98-1 XML_2.5-1
>>
>>
>>
>>> Dear BiomaRt developers,
>>>
>>> The following code using biomaRt sometimes produces error but sometimes not.
>>> Could you please help me to resolve the issue? Thanks a lot for your help!
>>>
>>> Library(biomaRt)
>>> mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
>>> seq1 = getSequence(id = "ENSDARG00000054562",
>>> type = "ensembl_gene_id", seqType = "gene_exon_intron",
>>> upstream = 350, mart = mart)
>>> Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"), :
>>>> Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT
>>>> FOUND
>>> FYI, this error also occurs in the development version of R.
>>>
>>> Best regards,
>>>
>>> Julie
>>>
>>> sessionInfo()
>>> R version 2.9.0 (2009-04-17)
>>> i386-apple-darwin8.11.1
>>>
>>> locale:
>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] biomaRt_2.0.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] RCurl_0.94-1 XML_2.3-0
>>>
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Best wishes
Wolfgang
------------------------------------------------
Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber
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