[ensembl-dev] CDS Incomplete status

[Konrad Karczewski]

Hello!

Thanks! This has helped quite a bit, though at an understandable cost of
performance.

In particular, the attributes do not seem to be in the VEP cache - are
there any plans to add these? It seems like they shouldn't take up too much
space on the scheme of things.

-Konrad

On Mon, Apr 28, 2014 at 8:27 AM, mag <mr6 at ebi.ac.uk> wrote:

>  Hi Konrad,
>
> The transcript object supports a method called 'transleatable_seq'.
> This will return the translateable part of a transcript.
> You can then apply the length method on the returned string.
>
> The CDS incomplete status is only available for manually annotated genes
> (coming from Havana).
> They know there is a protein-coding transcript, but the evidence available
> does not allow for full annotation of the sequence.
> These transcripts are flagged with the attribute 'cds_start_NF' or
> 'cds_end_NF'
> You can retrieve this for each transcript using
> $transcript->get_all_Attributes('cds_start_NF')
> or retrieve all the transcripts for a given attribute using
> $attribute_adaptor->fetch_all_by_Transcript(undef, 'cds_start_NF')
>
>
> Hope that helps,
> Magali
>
>
> On 24/04/2014 21:47, Konrad Karczewski wrote:
>
> 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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