I am running the biomart-perl script obtained from github (If it matters I am using Perl v5.12.4). All Biomart-perl dependencies are installed and everything seems to be working fine. (If irs, Perl v5.12.4)
EXCEPT..
I am having issues obtaining 5'upstream region of the longest transcript (Ensembl ID ENST00000372310) of the HSAPI SLC6A9 gene using the biomart-perl api. I simply do not get any output when using the perl script obtained from BioMart web interface. Basically I get no output with..
$query->setDataset("hsapiens_gene_ensembl");
$query->addFilter("ensembl_transcript_id", ["ENST00000372310"]);
$query->addFilter("upstream_flank", ["2000"]);
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("coding_transcript_flank");
$query->addAttribute("external_gene_id");
$query->addAttribute("strand");
Using the following registry
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartURLLocation
database="ensembl_mart_75"
default="1"
displayName="ENSEMBL GENES 75 (SANGER UK)"
host="www.biomart.org"
includeDatasets=""
martUser=""
name="ensembl"
path="/biomart/martservice"
port="80"
serverVirtualSchema="default"
visible="1" />
<MartURLLocation
database="sequence_mart_75"
default="0"
displayName="ENSEMBL SEQUENCE 75 (SANGER UK)"
host="www.biomart.org"
includeDatasets=""
martUser=""
name="sequence"
path="/biomart/martservice"
port="80"
serverVirtualSchema="default"
visible="0" />
<MartURLLocation
database="snp_mart_75"
default="0"
displayName="ENSEMBL VARIATION 75 (SANGER UK)"
host="www.biomart.org"
includeDatasets=""
martUser=""
name="snp"
path="/biomart/martservice"
port="80"
serverVirtualSchema="default"
visible="1" />
</MartRegistry>
However using the same registry as above, and the following, I am able to get the FASTA output for 5UTR of the transcript
$query->setDataset("hsapiens_gene_ensembl");
$query->addFilter("ensembl_transcript_id", ["ENST00000372310"]);
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("external_gene_id");
$query->addAttribute("strand");
$query->addAttribute("5utr");
I am not really sure what I am missing, anything wrong with my registry file?