[ensembl-dev] Transcript coordinates

Jens Christian Nielsen jcfnielsen at gmail.com
Mon Mar 11 15:59:44 GMT 2013

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

my @vfs = @{$vfa-> fetch_all_by_Slice_SO_terms($slice,
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

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