<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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