[BioC] Get genomic sequences

[Cei Abreu-Goodger]

Hi Johannes,

I thought 'getSequence' from the biomaRt package should allow you to do 
what you want. But, I can't seem to get it to work for genomic 
coordinates either:

library(biomaRt)
ens <- useMart("ensembl","hsapiens_gene_ensembl")
getSequence(chromosome=1,start=10000,end=11000, seqType="genomic", mart=ens)

Error in getSequence(chromosome = 1, start = 10000, end = 11000, seqType 
= "genomic",  :
   Please specify the type of sequence that needs to be retrieved when 
using biomaRt in web service mode.  Choose either gene_exon, 
transcript_exon,transcript_exon_intron, gene_exon_intron, cdna, 
coding,coding_transcript_flank,coding_gene_flank,transcript_flank,gene_flank,peptide, 
3utr or 5utr

 > sessionInfo()
R version 2.10.0 (2009-10-26)
i386-apple-darwin9.8.0

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices datasets  utils     methods
[8] base

other attached packages:
[1] biomaRt_2.2.0 Biobase_2.6.0

loaded via a namespace (and not attached):
[1] RCurl_1.2-1 XML_2.6-0


Cheers,

Cei

Johannes Waage wrote:
> Hi all,
> 
> Is there a way to fetch genomic sequences via Bioconductor directly? (Using
> galaxy, but I would like to automate)
> 
> I tried rtracklayer and biomaRt - rtracklayer doesn't seem to have an
> interface for fetching sequences, and biomaRt only seems to fetch sequences
> from a subset of gene ID's, while I just to need to fetch sequence from a
> genomic range.
> 
> fetchSequence(chr, strand, start, end) -> sequence
> 
> Any suggestions?
> 
> Thank you in advance!!
> 
> Best regards,
> JW,
> Uni. of Copenhagen
> 
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