Entering edit mode
9.9 years ago
pld
5.1k
I am trying to use ensembl's BioMart API to download seqeuences, but it fails on the following query:
$query->setDataset("hsapiens_gene_ensembl");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("cdna");
$query->formatter("FASTA");
With the following error message:
Attribute 'cdna' not found in dataset default.hsapiens_gene_ensembl
Trace begun at /usr/local/apps/Biomart/biomart-perl/lib/BioMart/Registry.pm line 490
BioMart::Registry::getAttribute('BioMart::Registry=HASH(0x3bd9f00)', 'hsapiens_gene_ensembl', 'cdna', 'default', 'default') called at /usr/local/apps/Biomart/biomart-perl/lib/BioMart/Query.pm line 1243
BioMart::Query::addAttribute('BioMart::Query=HASH(0x3be8a68)', 'cdna') called at pull-annos2.pl line 157
main::biomart_get_trans_seq('BioMart::Registry=HASH(0x3bd9f00)', 'hsapiens_gene_ensembl') called at pull-annos2.pl line 211
I'm not sure what the problem is, all of the other queries I run that don't ask for sequence information work correctly, it is only when I try and pull sequence information down that there is any issue. Can someone point to my mistake?
Have a look at this thread, perhaps it's the same issue.
That seems to have been the issue. It looks like the GenomicSequence datasets are not totally supported, I'm getting errors about unimplemented methods...