[Biopython-dev] Accessing additional fields in ABI files

[Peter Cock]

Great - I've checked in the initial work to the main branch,
https://github.com/biopython/biopython/commit/b20f3641a5eaae5df1d25de5ece8b7d8db441e3e

Peter

On Thu, Jul 10, 2014 at 9:40 AM, Mike Cariaso <cariaso at gmail.com> wrote:
> no thanks are necessary (quite the reverse), but they are welcomed.
>
>
> On Thu, Jul 10, 2014 at 9:25 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>> Hello from the pre-BOSC Codefest, where Bow and I have been
>> looking at the Bio.SeqIO ABI parser in response to an email from
>> Mike & David (CC'd, see below).
>>
>> All the different versions of the ABI capillary sequencers record
>> additional tags to the binary file which would record all sorts of
>> extra information like voltages and the raw colour data.
>>
>> Mike & David wanted access to some of this data, but the SeqIO
>> parser was not exposing it. Our proposal is to add a new dictionary
>> to the SeqRecord's annotations containing all the raw data so that
>> advanced users can do further processing.
>>
>> I'm going to work on this code today, adding a few more tests etc.
>>
>> Mike & David - are you happy to be thanked by name in the
>> commit comment (e.g. "With input from ...")?
>>
>> Mike - I am intending to incorporate your test file A6_1-DB3.ab1
>> into the Biopython unit test collection.
>>
>> Thanks,
>>
>> Peter
>>
>> ---------- Forwarded message ----------
>> <snip>