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

[Oliver, Gavin]

Hi Will.

Thanks.

I'm not certain what the method is doing though.

I did this: 


my $transcript =
$transcript_adaptor->fetch_by_stable_id('ENST00000297564');
my $trmapper = Bio::EnsEMBL::TranscriptMapper->new($transcript);

my  @coords = $trmapper->genomic2cdna( 100890372, 100905895, -1 );

foreach my $thing (@coords) {
        print $thing->start."\t".$thing->end."\n";
}

And get the following:

1       29
100904281       100905866
30      174
100899847       100904135
175     303
100890494       100899717
304     425

The method doesn't seem to do anything with my input coordinates.

But then I could well be missing something :)

Gavin

-----Original Message-----
From: Will Spooner [mailto:whs at eaglegenomics.com] 
Sent: 08 November 2010 16:29
To: Oliver, Gavin
Cc: dev at ensembl.org
Subject: Re: [ensembl-dev] Converting genomic coordinates to
transcript/exon etc

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
>  
>  
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com