Hi Mathias,
Could you try to run your query on v46 ?
I think I have spotted something odd in v47, but I need some time to
investigate. Meanwhile please try on v46, and get back to me if you see
the same error on v46.
Regards,
Benoit
Wahl, Matthias wrote:
Hi all ,
I am using Biomart to retrieve pairwise or multiple genome alignments.
The following query:
my $query =
BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');
$query->addFilter("mmus_dnafrag_start", ["1"]);
$query->addFilter("mmus_chro", ["1"]);
$query->addFilter("mmus_dnafrag_end", ["10000000"]);
$query->addAttribute("pairwise_genomic_alignments");
Works for pairwise genomic alignments
$query->setDataset("compara_mart_blastznet_hsap_mmus");
$query->addAttribute("pairwise_genomic_alignments");
but not for multiple genomic alignments
$query->setDataset("compara_mart_gerp_10species");
$query->addAttribute("multiple_genomic_alignments");
The line $query->addFilter("mmus_chro", ["1"]); results in the error
message
Filter 'mmus_chro' not found in dataset default.compara_mart_gerp_10species
How can I set the chromosome so that I do not get alignments for the
specified regions on all chromosomes?
Thank you very much!
Matthias
Matthias Wahl, PhD
Stowers Institute for Medical Research
1000 E. 50th Street
Kansas City, MO 64110
Phone: 816-926-4302
Fax: 816-926-2044
E-mail : [EMAIL PROTECTED]
_http://www.stowers-institute.org/_
--
Benoit Ballester, PhD
Ensembl Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom
