[Biopython-dev] SeqIO Abi Parser

Peter Cock p.j.a.cock at googlemail.com
Tue Jul 26 09:59:33 UTC 2011

On Tue, Jul 26, 2011 at 10:08 AM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> Hi everyone,
> A few weeks ago I wrote about my interest in making Biopython able to parse
> the Abi trace file. I've finished writing the SeqIO plugin and some tests. I
> thought this would be useful to a number of people, so I was wondering about
> what I should do after this (how will my code be reviewed?, should I just go
> with a pull request?). Of course, there are things that I might have missed
> when writing the plugin, so feel free to criticize/comment :)!
> Here's the SeqIO plugin:
> https://github.com/bow/biopython/blob/seqio-abi/Bio/SeqIO/AbiIO.py
> Looking forward to the reply,

Hi Wibowo,

You could send a pull request if you wanted, but this email to the dev list
is enough. I probably wouldn't just merge it - I prefer to rebase to the
current master first to get a clean history (especially if there are already
several merges in the branch history).

I will review your work.

In particular I plan to cross test with EMBOSS seqret to verify you produce
the same sequence and the same PHRED quality scores - this could be
done in test_Emboss.py

Thanks for your work!


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