[ensembl-dev] Converting cDNA position to genomic position!

[Will McLaren]

Hello Oyediran,

You will need to use a TranscriptMapper object;
http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1TranscriptMapper.html

The method you should use is cdna2genomic. Note that this returns an array
of coordinate objects; this is useful to know if, for example, your
coordinates only partially overlap the transcript.

Here's a bit of code to get you started:

my $reg = 'Bio::EnsEMBL::Registry';
$reg->load_registry_from_db(-host => 'ensembldb.ensembl.org',-user =>
'anonymous');

my $ta = $reg->get_adaptor('human','core','transcript');

my $t = $ta->fetch_by_stable_id('ENST00000373968');

my $mapper = Bio::EnsEMBL::TranscriptMapper->new($t);

@coords = $trmapper->cdna2genomic( 123, 554 );

Regards

Will McLaren
Ensembl Variation


On 15 November 2012 10:45, Oyediran Akinrinade <
oyediran.akinrinade at helsinki.fi> wrote:

>
>
> Hello,
>
> I have a list of ensembl transcripts IDs with their corresponding cDNA
> positions and I will like to get their genomic positions using the
> ensembl API. I have no experience with perl although I have
> installed ensembl-api on my mac computer. There are about 6000 IDs
> that I will like to get their genomic cordinates/positions, and
> web-based queries will not be the best solution. To this end, I
> write to request for your assistance.
>
> Looking forward to hearing from you soonest.
>
> Thanks,
>
> -Oyediran
>
>
>
>
>
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