[ensembl-dev] Converting genomic coordinates to transcript/exon etc

[Will Spooner]

Hi Gavin,

Take a look at Bio::EnsEMBL::TranscriptMapper;

my $trmapper = Bio::EnsEMBL::TranscriptMapper->new($transcript);
  @coords = $trmapper->cdna2genomic( 123, 554 );
  @coords = $trmapper->genomic2cdna( 141, 500, -1 );
  @coords = $trmapper->genomic2cds( 141, 500, -1 );
  @coords = $trmapper->pep2genomic( 10, 60 );
  @coords = $trmapper->genomic2pep( 123, 400, 1 );

Where @coords are Bio::EnsEMBL::Mapper::Coordinate and Gap objects.

Best,

Will


On 8 Nov 2010, at 16:04, Oliver, Gavin wrote:

> Hi all,
>  
> Using the funcgen API, if I know a probe feature maps to exon 2 of transcript A and the genomic coordinates are chromosome X bases 99-110…
>  
> ..how do I convert the genomic coordinates to transcript coordinates?
>  
> I have been reading the docs but I’m lost to be honest.
>  
> Gavin
>  
>  
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--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com