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@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@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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