Question: Biomart Perl API and obtaining upstream flanking sequences
0
gravatar for Livingstone Fultang
5.2 years ago by
United Kingdom
Livingstone Fultang0 wrote:

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? 

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Livingstone Fultang0
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