[ensembl-dev] Transcript coordinates

[Will McLaren]

Hi Jens,

The $tv transcript variation objects carry the coordinates in CDS,
cDNA and protein systems:

print "cdna coords: ", $tv->cdna_start, '-', $tv->cdna_end, "\n";
    print "cds coords: ", $tv->cds_start, '-', $tv->cds_end, "\n";
    print "pep coords: ", $tv->translation_start,
'-',$tv->translation_end, "\n";

You can also use a transcript mapper to convert between coordinate types:

http://www.ensembl.org/info/docs/Doxygen/core-api//classBio_1_1EnsEMBL_1_1TranscriptMapper.html

Regards

Will

On 11 March 2013 15:59, Jens Christian Nielsen <jcfnielsen at gmail.com> wrote:
> I am extracting transcripts and missense SNP's from a list of accession
> numbers, but I am having trouble mapping the genome coordinates to the aa
> position in the transcript. Is their a smart way to extract the position of
> the aa mutation counting from the begining of the transcript, so i can
> locate exactly which aa's that are prone to mutations. It seems kind of
> cumbersome to identify positions through the genome coordinates.
>
> This is a piece of my code where i right now am extracting the genome
> coordinates:
>
> my @vfs = @{$vfa-> fetch_all_by_Slice_SO_terms($slice,
> ['missense_variant'])};
> foreach my $vf (@vfs) {
> my $transcript_variations = $vf->get_all_TranscriptVariations;
>
> if (defined $transcript_variations){
> foreach my $tv (@{$transcript_variations}){
> if (defined $tv->pep_allele_string) { # the AA change
> print $tv->pep_allele_string."\t";
> }
> print $vf->seq_region_name, ":", $vf->start,"-",$vf->end."\n"; # print
> position in Ref in format
>                 }
>         }
> }
> Thanks in advance
>
> Jens
>
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