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Hi Konrad,<br>
<br>
The transcript object supports a method called 'transleatable_seq'.<br>
This will return the translateable part of a transcript.<br>
You can then apply the length method on the returned string.<br>
<br>
The CDS incomplete status is only available for manually annotated
genes (coming from Havana).<br>
They know there is a protein-coding transcript, but the evidence
available does not allow for full annotation of the sequence.<br>
These transcripts are flagged with the attribute 'cds_start_NF' or
'cds_end_NF'<br>
You can retrieve this for each transcript using
$transcript->get_all_Attributes('cds_start_NF')<br>
or retrieve all the transcripts for a given attribute using
$attribute_adaptor->fetch_all_by_Transcript(undef,
'cds_start_NF')<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 24/04/2014 21:47, Konrad Karczewski
wrote:<br>
</div>
<blockquote
cite="mid:2BD172D4-35FF-4DA1-A946-3DBE2D7C6FFA@broadinstitute.org"
type="cite">
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Hello!
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div>my $transcript_cds_length =
$transcript_variation->transcript->cdna_coding_end -
$transcript_variation->transcript->cdna_coding_start + 1;</div>
<div><br>
</div>
<div>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. <a
moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000162458;r=1:16084441-16091522;t=ENST00000510929">http://www.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000162458;r=1:16084441-16091522;t=ENST00000510929</a>).
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?</div>
<div><br>
</div>
<div>And side note, is this the best way to get transcript length?
I couldn't seem to find a direct reference to the length.<br>
<div><br class="webkit-block-placeholder">
</div>
<div apple-content-edited="true">
<div style="color: rgb(0, 0, 0); letter-spacing: normal;
orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
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word-wrap: break-word; -webkit-nbsp-mode: space;
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<div style="color: rgb(0, 0, 0); font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Thanks!<br
class="Apple-interchange-newline">
-Konrad</div>
</div>
</div>
<br>
</div>
<br>
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