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/
