[Biopython-dev] SeqIO Abi Parser

[Wibowo Arindrarto]

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. I
didn't have "EMBOSS_ROOT" in my os.environ paths (I installed 6.4.0 from
source, by the way), so this must be what's causing it. Is there another way
to automatically detect EMBOSS_ROOT other than this? Or perhaps we should
avoid emboss 6.4.0's bug by only checking if the id is EMBOSS_001? The only
case I think this would fail is if the user inputs "EMBOSS_001" before the
sequencing run as the sample id, which is possible but unlikely.

- 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).

- Other than those two, everything's tip top :).


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


On Tue, Aug 2, 2011 at 20:03, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Tue, Aug 2, 2011 at 6:57 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > On Tue, Aug 2, 2011 at 5:53 PM, Wibowo Arindrarto
> > <w.arindrarto at gmail.com> wrote:
> >> Hi Peter,
> >> I noticed that bug was because I did not add the _bytes_to_string()
> >> converter for a data type. I already fixed this with my latest push,
> adding
> >> the appropriate if clause at AbiIO.py:293-294.
> >> Regards,
> >
> > Was that only half the fix? This made it work for me:
> >
> >
> https://github.com/peterjc/biopython/commit/8fc1e141173a735740f91a1338a3fbb747fa2a45
> >
> > and:
> >
> >
> https://github.com/peterjc/biopython/commit/a44e206e482ca5904b395aaca3576a232769ce2e
> >
> > Peter
> >
>
> Could you test this branch, which I think is ready to be merged to the
> trunk now:
>
> https://github.com/peterjc/biopython/tree/seqio-abi
>
> Thanks,
>
> Peter
>