[Biopython-dev] SeqIO Abi Parser

[Wibowo Arindrarto]

Hi Peter,

On Wed, Aug 3, 2011 at 16:04, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, Aug 3, 2011 at 1:14 PM, Wibowo Arindrarto
> <w.arindrarto at gmail.com> wrote:
> > Hi Peter,
> > My bad, I forgot to change that one line and didn't test before
> comitting.
> > Thanks for fixing it.
> > I've ran the tests on your tree on py2.6.5 and py3.1.2, here are the
> > results:
> > - On both py2.6.5  and py3.1.2, I have the following test case error:
> > "NameError: global name 'embossversion' is not defined", on line 257.
> >...

It was simpler than that - I'd checked it in with a typo, emboss_version
> was what I wanted. Sorry about that confusion!


Silly me, I should've noticed you used emboss_version when I was looking at
the code checking Emboss dependency :/.



> > - On a related note, I noticed you set the minimum Emboss requirement to
> > 6.1.0 patch 3. I'm not sure if this the one I use previously, but my
> > previous Emboss 6.1.0 installation failed to extract the proper quality
> > values. Perhaps we should set the minimum version to 6.3.1? (well, making
> it
> > the only Emboss version that works with Biopython because of that 6.4.0
> > bug).
>
> We test a lot of FASTQ stuff which requires 6.1.0 patch 3 or later,
> which is why that requirement exists. Asking for at least EMBOSS
> 6.3.1 makes no practical difference as far as I can see.
>
> If you meant require EMBOSS 6.4.1 that hasn't been released yet.
>
> I'm expecting them to release EMBOSS 6.4.0 patch 1 soon (after
> I've tested the proposed patch Peter Rice sent), but that will still
> report itself as EMBOSS 6.4.0 (based on past patch behaviour,
> something I consider annoying but have to live with).


I meant Emboss 6.3.1, since that seems to be one that works best with the
current AbiIO implementation. But yeah, I guess as long as the tests work
it's fine.


> > - Other than those two, everything's tip top :).
> >
>
> Great. I've pushed the code to the main repository, and have
> just set off the buildbot slaves as a final sanity test.
>
> This reveal a minor Python 2.4 breakage (not a big issue - it only
> seems to be me still trying to keep testing this - and I'm about
> ready to give up), and another probable EMBOSS bug in an
> older version installed on one buildslave.
>
> Congratulations, your code will be in the next Biopython release.
>
> Thank you,
>
> Peter
>

This really made my day :)! You're welcome and thank you reviewing my code,
too!


Regards,
---
Wibowo Arindrarto (bow)
http://bow.web.id