[ensembl-dev] genomic2pep and pep2genomic

[Hardip Patel]

Hi All

I am trying to identify the codon triplet in which a single nucleotide genomic position is involved in.

Rephrased more elaborately,

I have genomic loci chr1:11863085:11863085:-1 (chr start end and strand).
This loci is overlapping with transcript ID: ENST00000413656.
The loci is in the protein-coding (CDS) region of the transcript/cDNA.

Therefore I first call transcript object by stable id using the transcript adaptor.
Then I identify the peptide co-ordinates for the genomic loci by calling transcriptmapper.
Once I get the peptide coordinate, I get the genomic coordinates for that peptide.

Below is the script to do so.

my $transcript_adaptor = $reg->get_adaptor("Human", "Core", "Transcript");
my $slice_adaptor = $reg->get_adaptor("Human", "Core", "Slice");
my $transcriptObject = $transcript_adaptor->fetch_by_stable_id("ENST00000413656");
my $transcriptMapper = $transcriptObject->get_TranscriptMapper();
my @pepCoords = $transcriptMapper->genomic2pep(11863085, 11863085, -1);
foreach my $pepinfo (@pepCoords){
  my @pep2genomic = $transcriptMapper->pep2genomic($pepinfo->start, $pepinfo->end);
  print "Peptide = ". $pepinfo->start."\t". $pepinfo->end."\t". $pepinfo->id."\t". $pepinfo->length."\t". $pepinfo->strand."\n";
  foreach my $gc (@pep2genomic){
    my $codonSlice = $slice_adaptor->fetch_by_region("toplevel", 1 , $gc->start, $gc->end, $gc->strand);
    print "Genomic = ".$gc->start."\t".$gc->end."\t".$gc->id."\t".$gc->length."\t".$gc->strand."\t".$codonSlice->seq."\n";
  }
}

However, normally a peptide should represent three nucleotides, but I am getting a two nucleotide codon (TC) for this position and my script dies with following error message

Can't locate object method "id" via package "Bio::EnsEMBL::Mapper::Gap".

Could somebody please explain me what these gaps are? And also, how to overcome this issue of two/one nucleotide codons.

Any help is greatly appreciated

Thanking you

Hardip
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