Hi Alexandre, On Fri, 2008-07-25 at 09:05 +0200, Alexandre Gattiker wrote: > Thank you very much, that (mostly) solved it! > > I can now retrieve transcript/gene/etc. sequences. But if I select one > of the four Flank options, I get a blank result and a warning in the log: > Use of uninitialized value in concatenation (.) or string at > biomart-perl/lib/BioMart/Web.pm line 2446
Ok, this is probably because the warning message isnt getting propagated correctly over the webservice. Can you configure your apache using <MartDBLocation >.... </MartDBLocation> type connection params in your registry instead of <MartURLLocation>. I sent you these in my first email yesterday. That will connect you to ensembl public databases directly instead of going via www.biomart.org. I am hoping this would resolve the flanks problem. > Running the same query at biomart.org however yields a screen message > and alert box: > Validation Error: Requests for flank sequence must be accompanied by an > upstream_flank or downstream_flank request > > <http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=mmusculus_gene_ensembl.default.sequences.gene_stable_id|mmusculus_gene_ensembl.default.sequences.str_chrom_name|mmusculus_gene_ensembl.default.sequences.struct_biotype|mmusculus_gene_ensembl.default.sequences.coding_gene_flank&FILTERS=mmusculus_gene_ensembl.default.filters.ensembl_gene_id."ENSMUSG00000055866"&VISIBLEPANEL=resultspanel> > > > Then, if I do select an upstream_flank, I still get a blank page, while the > query works at biomart.org: > <http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=mmusculus_gene_ensembl.default.sequences.gene_stable_id|mmusculus_gene_ensembl.default.sequences.str_chrom_name|mmusculus_gene_ensembl.default.sequences.struct_biotype|mmusculus_gene_ensembl.default.sequences.coding_gene_flank|mmusculus_gene_ensembl.default.sequences.upstream_flank."10"&FILTERS=mmusculus_gene_ensembl.default.filters.ensembl_gene_id."ENSMUSG00000055866"&VISIBLEPANEL=resultspanel> > > NB I'm using biomart embedded into Ensembl. > > > Another issue: > I'm trying to fetch the sequence around the transcription start site > (e.g. -2 kb to +2 kb) for promoter analysis. Is there a way to do that? You can only retrieve the +/- seqs w.r.t the start of first exon. TSS's coordinates I guess are not available in ensembl database. cc'ed Glenn to confirm. cheers syed > Best regards > Alexandre > > > Syed Haider wrote: > > an even better solution, just add this to your existing registry: > > > > <MartURLLocation > > name = "sequence" > > displayName = "Sequence (release 49)" > > host = "www.biomart.org" > > port = "80" > > visible = "" > > default = "" > > includeDatasets = "mmusculus_genomic_sequence" > > martUser = "" > > /> > > > > > > On Thu, 2008-07-24 at 18:22 +0200, Alexandre Gattiker wrote: > > > >> Hello, > >> > >> Kudos for this great piece of software. I managed to whip up a very > >> functional biomart by mashing up some lab data with the Ensembl biomart, > >> almost accidentally, as I didn't even expect that to be possible! It's > >> rare enough that software works even better than advertised and in such > >> a modular way. > >> > >> I have a small issue, however. When I go to the Attributes -> Sequences > >> page, the SEQUENCES section has: > >> > >> No visible attributes in collection seq_scope_type > >> No visible attributes in collection upstream > >> No visible attributes in collection downstream > >> > >> I assume that's linked to warnings I get running configure.pl: > >> > >> Setting possible links between datasets > >> ....(scanning) 33% WARNING: Pointer attributes from > >> mmusculus_genomic_sequence will not be available as > >> mmusculus_genomic_sequence not in registry > >> WARNING: Pointer attributes from mmusculus_genomic_sequence will > >> not be available as mmusculus_genomic_sequence not in registry > >> WARNING: Pointer attributes from mmusculus_genomic_sequence will > >> not be available as mmusculus_genomic_sequence not in registry > >> > >> My config is as follows. I have biomart 0.7. > >> > >> <MartURLLocation > >> name = "ensembl" > >> displayName = "Ensembl Genes (release 49)" > >> host = "www.biomart.org" > >> port = "80" > >> visible = "1" > >> default = "" > >> includeDatasets = "mmusculus_gene_ensembl" > >> martUser = "" > >> /> > >> > >> I tried > >> includeDatasets = "mmusculus_gene_ensembl,mmusculus_genomic_sequence" > >> but that didn't solve the problem. I also tried to leave includeDatasets > >> empty but I still get the warning (now for all species). > >> > >> Best, > >> Alexandre > >> > >> > > -- > > ====================================== > > Syed Haider. > > EMBL-European Bioinformatics Institute > > Wellcome Trust Genome Campus, Hinxton, > > Cambridge CB10 1SD, UK. > > ====================================== > > > > > > > > Richard Holland <[EMAIL PROTECTED]> > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
