[Biojava-dev] Extended ABIF Parser and SCF Writer

[Franklin Bristow]

Hello,
I think I like the idea of having a module for the I/O of sequencers in
general.  I really only have familiarity with ABI sequencers (ie: 31xx and
37xx) and the data that they spit out, so I would be able to offer some help
there.  Needless to say, the documentation that ABI released regarding their
binary format was much appreciated when I was going through the code.

To Micha:  when you talk about 'during I/O', do you mean having some kind of
an event based parser?  When I wrote my extended ABIF parser I modelled it
after the perl module Bio::Trace::ABIF, so there are accessors for many of
the tags that are defined in the ABI spec.

On Tue, Jul 7, 2009 at 12:08 PM, Micha Sammeth <gmicha at gmail.com> wrote:

> Hi,
>
> the time I worked on SCF and ABI files is a bit ago, but lets see if I can
> contribute something here. Working since a year on NGS, I could imagine that
> readers for the standard-output of pipelines by Illumina & Co would also fit
> there.
>
> If there is a reader module, I would plead for a low-level interface for
> accessing sequences/qualities and re-usable data containers during I/O. But
> maybe that is rather an early stage to talk about that when not even the
> existence of the module is decided.
>
> cheers - micha.
>
>
> Andreas Prlic wrote:
>
>> Hi Franklin,
>>
>> The theme of the moment is modularization... I wonder if we should make a
>> module for parsing the output of sequencers...
>>
>> This topic is also a bit related to the discussion we had around BOSC last
>> week, how to contribute modules, and what is the role of a module
>> maintainer. I will send out a more detailed summary on that a bit later.
>>
>> Andreas
>>
>>
>> On Tue, Jul 7, 2009 at 6:34 AM, Franklin Bristow <fbristow at gmail.com>
>> wrote:
>>
>>  Hi everyone,
>>> Now that you're all back from ISMB (I hope you all had a good time!) I
>>> thought it would be a good time to bring this up.
>>>
>>> A while back I wrote to the list about an ABIF parser and SCF writer that
>>> I
>>> had written.  I got some pointers on things to change and I've since made
>>> the suggested changes.  Now I was wondering how I should go about getting
>>> these files into BioJava....
>>>
>>> --
>>> Franklin
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>
>
>


-- 
Franklin