[ensembl-dev] CDS Incomplete status

[Konrad Karczewski]

Hello!

I've been using the API to get the length of the coding portion of a transcript and I think I figured out the best way is:

my $transcript_cds_length = $transcript_variation->transcript->cdna_coding_end - $transcript_variation->transcript->cdna_coding_start + 1;

However, for some transcripts, this number is not a multiple of 3 (though it is approximately correct - within 2 bp of the number of AA's of the transcript * 3). It seems to happen when there is a "CDS Incomplete" status on the transcript (e.g. http://www.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000162458;r=1:16084441-16091522;t=ENST00000510929). I would have thought if the CDS were incomplete then "cdna_coding_end" or "cdna_coding_start" would be undefined - is there another way to get the CDS Incomplete status?

And side note, is this the best way to get transcript length? I couldn't seem to find a direct reference to the length.

Thanks!
-Konrad

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