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
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?
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]>
--
--------------------------------------------------------
Alexandre Gattiker Bioinformatics & Biostatistics Core Facility
EPFL School of Life Sciences / Faculté des Sciences de la vie FSV
http://people.epfl.ch/Alexandre.Gattiker
