[ensembl-dev] [SPAM] - Re: Converting genomic coordinates to transcript coordinates - Email found in subject

[Oliver, Gavin]

Thanks Will - that has done the trick!

 

Best, 

 

Gavin

 

________________________________

From: wmclaren at gmail.com [mailto:wmclaren at gmail.com] On Behalf Of Will
McLaren
Sent: 26 January 2011 13:11
To: Oliver, Gavin
Cc: dev at ensembl.org
Subject: [SPAM] - Re: [ensembl-dev] Converting genomic coordinates to
transcript coordinates - Email found in subject

 

Hi Gavin,

 

You will need a transcript mapper object:

 

my $tm = $transcript->get_TranscriptMapper;

 

my @coords = $tm->genomic2cdna($start, $end, $strand);

 

This returns a list of Bio::EnsEMBL::Mapper::Coordinate and  
Bio::EnsEMBL::Mapper::Gap objects.

 

Cheers

 

Will

On 26 January 2011 12:46, Oliver, Gavin <gavin.oliver at almacgroup.com>
wrote:

Hi, 

 

I'm guessing the answer will be transfer or transform but can someone
advise on the fastest way to convert feature start/end coordinates from
genomic to transcript-based?  I don't want to mistakenly do it in an
unnecessarily time/resource-consuming manner.

 

Best, 

 

Gavin

 

  

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