[Biopython-dev] SeqIO Abi Parser

[Peter Cock]

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!

> - 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).

> - 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