<div dir="ltr">Hi Magali<div><br></div><div>I understand. I am happy with this methods already... and I understand how they could lead misleading errors. </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 11:41, 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>
There are currently no plans on implementing this at the gene object
level.<br>
<br>
To be fair, I am not entirely convinced about the value of getting
this relatively transcript specific information via the gene object.<br>
Within the same gene, two transcripts could share an exon, ie
overlap the same genomic location.<br>
However, this exon could be coding in one transcript and non-coding
in the other, or even regions of that same exon.<br>
In that case, get_all_CDS and get_all_UTRs would both have the same
genomic coordinates in their output, which could be misleading.<br>
<br>
<br>
Regards,<br>
Magali<div><div class="h5"><br>
<br>
<div>On 17/07/2015 11:18, Duarte Molha
wrote:<br>
</div>
<blockquote type="cite">
<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><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><br>
<br>
<div>On 16/04/2015 20:12, Duarte Molha wrote:<br>
</div>
</span>
<blockquote type="cite">
<div dir="ltr"><span>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><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>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>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><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><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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