[BioC] getSequence from biomaRt changes the order of sequences given as input - is it normal?

[Emmanuel Levy]

Dear Steffen,

Thank you for your answer, I'll send a suggestion to users at biomart then.

In the meantime it's really not a problem indeed, the function "match"
enables one to reorder things easily.

All the best,

Emmanuel


On 7 January 2013 21:12, Steffen Durinck <durinck.steffen at gene.com> wrote:
> Hi Emmanuel,
>
> biomaRt returns you the results as they get passed back from the BioMart
> servers and does no reordering.
> If you want this changed, this could be a suggestion for the BioMart mailing
> list  users at biomart.org.
> If the order of BioMart server results would be ordered according to the
> query input then that would be reflected in the biomaRt results.  However
> this would complicate queries for example if you have multiple filters then
> one would have to start indicating according to which filter results should
> be ordered.
>
> For now I would reorder the output in R if that is what you need.
>
> Cheers,
> Steffen
>
> On Mon, Jan 7, 2013 at 10:40 AM, Emmanuel Levy <emmanuel.levy at gmail.com>
> wrote:
>>
>> Hello,
>>
>> I started using biomaRt and find it really convenient. One thing I
>> noticed is that the function getSequence reorders the sequences when
>> multiple ids are given as input.
>>
>> I'm not sure if this is normal or if I missed an option?
>>
>> Here is what I do:
>>
>> > ensembl.yeast = useMart(biomart="ensembl", dataset =
>> > "scerevisiae_gene_ensembl")
>> > ids = c("S000005528","S000000221" ,"S000005993", "S000003105",
>> > "S000004200")
>> > yeast.gen = getSequence( id=ids, mart=ensembl.yeast, seqType=c("cdna"),
>> > type="sgd_transcript" )
>> > yeast.gen[[2]]
>> [1] "S000005528" "S000004200" "S000003105" "S000000221" "S000005993"
>>
>> So the ID No. 5 is now No. 2. It would be convenient if the sequences
>> retrieved would be in the order specified by "id". Not that it's a big
>> problem but just a thought ... or maybe I missed something?
>>
>> All the best,
>>
>> Emmanuel
>>
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>
>