> From: Arek Kasprzyk [mailto:[EMAIL PROTECTED] > On 9 May 2006, at 21:11, Amir Karger wrote: > > you need to watch for attributes which are named as follows: > "dataset.attribute". These are so called pointer (placeholder) > attributes > and they refer to a different dataset from the one they > presented in so > in your example you cannot use them in hsapiens_gene_ensembl > but only > in > hsapiens_gene_ensembl_structure. > > This rather annoying arrangement for pointer attributes is > going to be > removed > in 0.5. > However for now > you need to either find the appropriate dataset for them yourself or > just > skip any with "dataset.attribute" format
Perhaps I'm missing something. I want to input HGNC gene names (like BRCA1) and get out FASTA sequences for all exons in those genes. I would like the header to have chromosome & gene ID along with exon start, end, strand. I'm able to do that in martView without selecting a second dataset. Does it magically work there, but not in biomart-plib (0.4)? Thanks, -Amir > > a. > > > > -------------------------------------------------------------- > ---------- > ------- > Arek Kasprzyk > EMBL-European Bioinformatics Institute. > Wellcome Trust Genome Campus, Hinxton, > Cambridge CB10 1SD, UK. > Tel: +44-(0)1223-494606 > Fax: +44-(0)1223-494468 > -------------------------------------------------------------- > ---------- > ------- > > > >
