<div dir="ltr">Hi Bertrand, Peter,<div><br></div><div>Hmmer 3.1 beta output is indeed not fully tested yet. This is more about making sure the small edge cases in the file format is covered, however, and thus I also expect no changes to the API in this regard.</div><div><br></div><div>There is still one issue in which the API *may* be affected, which is related to Issue 367 (<a href="https://github.com/biopython/biopython/issues/367">https://github.com/biopython/biopython/issues/367</a>). This may slightly change the way the HSPFragment object is represented when parsing exonerate files with split codons. I do not expect this to affect the other file formats, however.</div><div><br></div><div>So there are still two open issues at least, but no expected major API changes.</div><div><br></div><div>Do we have a timeline for the next release, by the way? I could possibly close those if there is still enough time..</div><div><br></div><div>Cheers,</div><div>Bow</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 12, 2015 at 11:31 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Bertrand,<br>
<br>
I don't think we're expecting any major changes to the API,<br>
although perhaps nucleotide-vs-protein and codon alignments<br>
might be one area where that is more likely.<br>
<br>
Bow - are you comfortable with removing the experimental<br>
warning for SearchIO yet? As I recall there was a couple of<br>
recent HMMER 3.1 beta output changes you were looking at...<br>
<span class="HOEnZb"><font color="#888888"><br>
Peter<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
On Mon, Oct 12, 2015 at 10:21 AM, Bertrand Neron <<a href="mailto:bneron@pasteur.fr">bneron@pasteur.fr</a>> wrote:<br>
> Hello,<br>
><br>
> I use in one script the SearchIO module to parse 'hmmer3-text',<br>
> it works well, but I have the following message.<br>
><br>
> "Bio.SearchIO is an experimental submodule which may undergo<br>
> significant changes prior to its future official release."<br>
><br>
> I'd like to release my script, so what is exactly the status<br>
> of this module, and it's future?<br>
><br>
> Thank you<br>
><br>
> Bertrand<br>
><br>
> --<br>
> Bertrand Néron<br>
> Software Engineer<br>
> Center of Informatics for Biology<br>
> (<a href="http://www.pasteur.fr/en/research/center-informatics-biology" rel="noreferrer" target="_blank">http://www.pasteur.fr/en/research/center-informatics-biology</a>)<br>
><br>
> Institut Pasteur<br>
> 28, Rue du Dr Roux<br>
> 75724 Paris cedex 15<br>
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