[Biopython] module SearchIO status

[Wibowo Arindrarto]

Hi Bertrand, Peter,

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.

There is still one issue in which the API *may* be affected, which is
related to Issue 367 (https://github.com/biopython/biopython/issues/367).
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.

So there are still two open issues at least, but no expected major API
changes.

Do we have a timeline for the next release, by the way? I could possibly
close those if there is still enough time..

Cheers,
Bow

On Mon, Oct 12, 2015 at 11:31 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Hi Bertrand,
>
> I don't think we're expecting any major changes to the API,
> although perhaps nucleotide-vs-protein and codon alignments
> might be one area where that is more likely.
>
> Bow - are you comfortable with removing the experimental
> warning for SearchIO yet? As I recall there was a couple of
> recent HMMER 3.1 beta output changes you were looking at...
>
> Peter
>
>
> On Mon, Oct 12, 2015 at 10:21 AM, Bertrand Neron <bneron at pasteur.fr>
> wrote:
> > Hello,
> >
> > I use in one script the SearchIO module to parse 'hmmer3-text',
> > it works well, but I have the following message.
> >
> > "Bio.SearchIO is an experimental submodule which may undergo
> > significant changes prior to its future official release."
> >
> > I'd like to release my script, so what is exactly the status
> > of this module, and it's future?
> >
> > Thank you
> >
> > Bertrand
> >
> > --
> > Bertrand Néron
> > Software Engineer
> > Center of Informatics for Biology
> > (http://www.pasteur.fr/en/research/center-informatics-biology)
> >
> > Institut Pasteur
> > 28, Rue du Dr Roux
> > 75724 Paris cedex 15
> > _______________________________________________
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>
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