<div dir="ltr">Any plans on implementing this at the gene object level?<div><br></div><div>It would be great if we could retrieve all this regions without needing to cycle through each transcript belonging to a gene of interest.</div><div><br></div><div>Many thanks </div><div><br></div><div>Duarte</div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br> Duarte Miguel Paulo Molha <br></font><div><font style="background-color:rgb(255,255,255)" color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</font></div></div></div>
<br><div class="gmail_quote">On 17 July 2015 at 07:56, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Duarte,<br>
<br>
As of this release (81), new methods are available from the transcript
object:<br>
- get_all_five_prime_UTR<br>
- get_all_three_prime_UTR<br>
- get_all_CDS<br>
<br>
These methods return a list of regions representing the
coding/noncoding regions of the transcript's exons.<br>
<br>
<br>
Hope that helps,<br>
Magali<span class=""><br>
<br>
<div>On 16/04/2015 20:12, Duarte Molha
wrote:<br>
</div>
</span><blockquote type="cite">
<div dir="ltr"><span class="">Thanks Kieron
<div><br>
</div>
<div>I understand your point of view... but I still think there
is a case for a couple of methods to be implemented in the
transcript object:</div>
<div>@{$transcript->get_coding_regions} and
@{$transcript->get_noncoding_regions} </div>
<div><br>
</div>
<div>Both returning feature objects. Am I the only one to find
these useful? I hope not :)</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
</div>
</span><div>Duarte</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div><span class=""><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br>
</font>
</span><div><font style="background-color:rgb(255,255,255)" color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
</div>
<br>
<div class="gmail_quote"><span class="">On 16 April 2015 at 16:19, Kieron
Taylor <span dir="ltr"><<a href="mailto:ktaylor@ebi.ac.uk" target="_blank">ktaylor@ebi.ac.uk</a>></span>
wrote:<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">Hi Duarte,<br>
<br>
The coordinates you’re getting back are pre-splicing. The
method you’re calling is from the Transcript class, hence
the response is with reference to that object. If you’re
after exon coordinates, you should be attempting to work
with exon objects, such as fetching the exons of the
transcript and asking them for
coding_region_start($transcript) until numbers start
appearing. Your workaround is also a valid approach.<br>
<br>
My explanation isn’t very satisfactory, but we try to avoid
writing methods that need complex return types, such as the
list of lists required for your usecase. More often than
not, users require other attributes of the objects too, so
you would still end up with a list of exons. I hope that
helps.<br>
<br>
Regards,<br>
<br>
Kieron<br>
<br>
<br>
Kieron Taylor PhD.<br>
Ensembl Core senior software developer<br>
<br>
EMBL, European Bioinformatics Institute<br>
</span><div>
<div><span class=""><br>
<br>
<br>
<br>
<br>
> On 16 Apr 2015, at 09:15, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>>
wrote:<br>
><br>
> Anyone able to provide me some help on this?<br>
><br>
> I have now found away around this issue by finding
the exonic regions within the reported URT, but would
very much like to understand the thinking behind this.<br>
><br>
> Best regards<br>
><br>
> Duarte<br>
><br>
><br>
> =========================<br>
> Duarte Miguel Paulo Molha<br></span>
> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a><br>
> =========================<span class=""><br>
><br>
> On 14 April 2015 at 13:40, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>>
wrote:<br>
> Dear Developers<br>
><br>
> Please consider the transcript :<br>
><br>
> ENST00000470357<br>
><br>
> I am trying to retrieve the coordinates of UTR
regions of this transcript<br>
> To this end I have a script that basicaly starts
with the transcript feature object $transcript<br>
><br>
> my $five_prime =
$transcript->five_prime_utr_Feature;<br>
><br>
> $feature_params->{start} =
$five_prime->start;<br>
> $feature_params->{end} = $five_prime->end;<br>
><br>
> However, in this case the script will output the
coordinates from the start of the 1st non_coding exon to
the end of the non-coding portion of the 3rd exon (chr1
7772707 7777171).<br>
> How can I change this so that the script will only
output the coordinates of the non-coding exon portions?<br>
><br>
> In this case I would like to output:<br>
><br>
> chr1 7772707 7773198<br>
> chr1 7773442 7773511<br>
> chr1 7777160 7777171<br>
><br>
> This there a simple way of achieving this?<br>
><br>
> Many thanks<br>
><br>
> Duarte<br>
><br>
><br>
</span></div>
</div>
<div>
<div>>
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