[Biopython-dev] SeqIO Abi Parser

Wibowo Arindrarto w.arindrarto at gmail.com
Fri Jul 29 08:07:43 UTC 2011

Hi Peter,

I made a local branch tracking your seqio-abi tree. I agree to most of the
changes, but I think I'm a bit lost on the filename part.

My intention is to use the filename of the Abi file as the ID for the
SeqRecord, instead of the stored records identified returned by seqret. The
reason is because it's easier to see which Abi file a SeqRecord came from by
looking at the ID (or output file name, in case the SeqRecord is written as
another format), since the records identifier data is not readily available.
I chose to store the records identifier in SeqRecord.name (sample_id), so
users can still cross check if they want to.

My 'except' block (AbiIO.py:83) is a bad way to deal with '.name' being
absent, now that I think of it. But do you think instead of 'None', maybe we
could use 'file_id = str(handle)' or 'file_id = self.name'?

And lastly, could you clarify what you mean by alphabet issue on

Wibowo Arindrarto (bow)

On Fri, Jul 29, 2011 at 01:01, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Tue, Jul 26, 2011 at 11:37 AM, Wibowo Arindrarto wrote:
> >
> > I'm looking forward to your review!
> >
> Hi Bow,
> I made a start tonight,
> https://github.com/peterjc/biopython/tree/seqio-abi
> I haven't added the ABI files to test_SeqIO.py yet,
> there is some alphabet issue to check there.
> I noticed that EMBOSS seqret (at least the old
> copy I had installed on my laptop, v6.1.0 I think)
> was able to give ABI records identifiers (rather
> than the hack of using the filename).
> Peter

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