[Open-bio-l] FASTQ in BioRuby?

[Peter]

On Thu, Aug 27, 2009 at 12:20 PM, Naohisa
GOTO<ngoto at gen-info.osaka-u.ac.jp> wrote:
>
> Hello Peter,
>
> sorry for responding too late. I've subscribed to open-bio-l,
> but I could not actively join to the discussions, because of
> lack of my knowledge about FASTQ.
>
> There is a small primitive code attempt to support FASTQ format
> in BioRuby, which is not yet merged in the main repository.
> http://github.com/ngoto/bioruby/tree/master
>
> Recently, Anthony Underwood contributed chromatgram classes
> to support SCF/ABI formats, which will be merged soon,
> after bug-fix maintenance release of 1.3.1.
> http://github.com/aunderwo/bioruby/tree/master
>
> I'm now planning to rewrite my FASTQ code to be consistent
> with the chromatgram classes, and with the open-bio standards.
>
> Thank you,
>
> Naohisa Goto

That is excellent news :)

I'm not sure how format names work in BioRuby, but if you
do have a set of format names as strings as we do in
Biopython, BioPerl and EMBOSS it would be nice to be
consistent here:

http://biopython.org/wiki/SeqIO
http://bioperl.org/wiki/HOWTO:SeqIO
http://emboss.sourceforge.net/docs/themes/SequenceFormats.html

There is some basic information on wikipedia, but this
does not go into detail:
http://www.bioperl.org/wiki/FASTQ_sequence_format

Please feel free to ask any questions about how we are
interpreting things.

Thank you,

Peter