<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jun 10, 2015 at 1:14 PM, Eric Talevich <span dir="ltr"><<a href="mailto:eric.talevich@gmail.com" target="_blank">eric.talevich@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><span class="">On Wed, Jun 10, 2015 at 2:18 AM, Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span>On Tue, Jun 9, 2015 at 8:17 PM, Eric Talevich <<a href="mailto:eric.talevich@gmail.com" target="_blank">eric.talevich@gmail.com</a>> wrote:<br>
> On Thu, Jun 4, 2015 at 3:44 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>><br>
> wrote:<br>
>><br>
>> This would be great to have merged - pathological test cases<br>
>> and interconversion too :)<br>
>><br>
>> Did we settle on a plan for parent/child relationships in<br>
>> SeqFeature objects (beyond deprecating sub_features<br>
>> which has been replaced with CompoundLocations)?<br>
>><br>
>> Peter<br>
><br>
><br>
> The last thread I see on this topic is from the end of summer 2012:<br>
> <a href="http://mailman.open-bio.org/pipermail/biopython-dev/2012-July/018979.html" target="_blank">http://mailman.open-bio.org/pipermail/biopython-dev/2012-July/018979.html</a><br>
> (thread)<br>
> <a href="http://mailman.open-bio.org/pipermail/biopython-dev/2012-September/019101.html" target="_blank">http://mailman.open-bio.org/pipermail/biopython-dev/2012-September/019101.html</a><br>
> (terminal)<br>
><br>
> I'm a bit confused because the CompoundLocation class exists in<br>
> Bio/SeqFeature.py, and git blame says it was written in late 2011 -- Peter's<br>
> Time Machine in action? Does the f_loc5 branch modify the existing<br>
> CompoundLocation class, then?<br>
<br>
</span>Old commits rebased to master; perhaps a merge would have<br>
been clearer? As far as I recall, f_loc5 or whatever the final<br>
iteration of this was, is all in the master now.<br></blockquote><div><br></div></span><div>That's great, I didn't realize this had landed already. Sorry for the confusion.<br><br></div><div>So I suppose the remaining tasks are, in no particular order:<br><br></div><div>- Add/port Brad's GFF-GenBank converters and tests to Biopython. Ensure all the tests pass.<br><br></div><div>- Enable GFF3 support by merging or porting from Brad's branch, bcbb/gff, or gffutils?<br></div><div><br></div><div>- See about merging Lenna's GSoC 2012 work. This was based on the f_loc4, not the landed f_loc5, so this won't be a clean merge. Further discussion needed.<br></div></div></div></div></blockquote><div><br></div><div>Fortunately, it's based on f_loc5 and should merge cleanly. I just rebased it today; my PR is still active. <a href="https://github.com/biopython/biopython/pull/309">https://github.com/biopython/biopython/pull/309</a><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div></div><span class=""><div><br><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
So I think we're ready to remove the sub_features attribute (and<br>
the associated code in the GenBank parser etc which populates it).<br></blockquote><div><br></div></span><div>Can we do that before deciding how to represent parent/child relationships?<br><br><br></div><span class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
What to add for parent/child relationships between features is<br>
yet to be decided.<span><br></span></blockquote></span></div><br></div><div class="gmail_extra">I wonder if we can follow the lead of one of the GFF implementations mentioned above.<br><br></div><div class="gmail_extra">Has this been discussed in a more recent thread that I didn't link here?<span class=""><font color="#888888"><br><br></font></span></div><span class=""><font color="#888888"><div class="gmail_extra">-Eric<br></div></font></span></div>
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