[Biopython-dev] SeqIO Abi Parser

[Wibowo Arindrarto]

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



On Tue, Aug 2, 2011 at 18:47, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Sat, Jul 30, 2011 at 8:42 AM, Wibowo Arindrarto
> <w.arindrarto at gmail.com> wrote:
> > Hi Peter,
> > I've done some more improvements to the code:
> > - I've written the check and unittest for the file handle mode. I've set
> it
> > so that abi file has to be opened in 'rb' mode, otherwise it'll return an
> > error. While it's ok to open in 'r' mode in python 2 in Linux, it has to
> be
> > specified as 'rb' in Windows and/or Python 3 for the file to be read
> > correctly. So I decided forcing it to 'rb' is the best. Because of this,
> I
> > changed 'test_SeqIO.py:503' to include the mode argument when opening.
>
> OK, good.
>
> > - I've also checked against test_Emboss.py for seqret output, after
> > including the abi format in it. My EMBOSS version is 6.4.0. There was a
> > slight problem with this testing, since for some reason the ID returned
> by
> > seqret is always "EMBOSS_001". Something might be wrong with my EMBOSS
> > installation, since when I previously tested it against 6.1.0, the ID was
> > correct (although the qual values not, so I had to upgrade). As expected,
> if
> > I comment out the code that tests for sequence id
> ('test_Emboss.py:168-172')
> > the tests pass. Maybe you could try testing it as well and see if EMBOSS
> > also returns the default id instead of the sample name?
>
> EMBOSS 6.3.1 is fine, so I think we should report this as a bug in EMBOSS
> 6.4.0
>
> > - Finally, I did some small cosmetic changes to the code (typos, etc).
> > All changes have been pushed to my github fork. Now I still have time for
> > the weekend to improve whatever needs to be improved :).
> > Regards,
>
> There appears to be another Python 3 problem, consider this at the
> python prompt:
>
> from Bio import SeqIO
> record = SeqIO.read("Tests/Abi/310.ab1", "abi")
> record.letter_annotations["phred_quality"]
>
> I expect as list of integers, e.g. [0, 0, 0, ..., 0] not ['\x00',
> '\x00', '\x00', ..., '\x00']
>
> Peter
>