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

[Will Spooner]

It's giving you the cdna coordinates of ENST00000297564 for your region 100890372..100905895. There are three exons (by the look of it), 1..29, 30..174, 175..303 and 304..425, and their corres[ponding genomic locations. 

Will



On 8 Nov 2010, at 17:28, Oliver, Gavin wrote:

> 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
> 
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William Spooner
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http://www.eaglegenomics.com