[Biopython-dev] Preparing for Biopython 1.50 (beta)

[Brad Chapman]

Hi David;

> I've got some 454 and Solid data you could test it on too.
> 
> Has anybody else looked into how these other two Next Gen formats might 
> complicate things?

Sweet. We definitely want to support output from them as well; it is 
great to have someone on board who is working with data from other
machines.

Peter did a pretty thorough investigation of the different formats
and wrote it up in the docs to the proposed QualityIO module:

http://github.com/peterjc/biopython-seqio-quality/blob/6fdf27393cb7318b229ff8587721e83544da968d/Bio/SeqIO/QualityIO.py

Does this make sense with your experience?

If you feel comfortable with git, Peter set up a new branch with his
code for this:

http://github.com/peterjc/biopython-seqio-quality/tree/master

and we'd be more than happy to have you testing it. Alternatively,
if you want to submit some smaller data files we can use in testing, you
could attach them to the current enhancement request:

http://bugzilla.open-bio.org/show_bug.cgi?id=2767

Thanks for the help,
Brad

> 
> Brad Chapman wrote:
> > Peter;
> >
> >   
> >> I think we should probably do another release soon 
> >>     
> >
> > Good call. +1 from me.
> >
> >   
> >> I'd like to include the following changes as part of the beta, but it
> >> would be sensible to have someone else try these out first.  Any
> >> volunteers?
> >>
> >> Bug 2767 - Bio.SeqIO support for FASTQ and QUAL files
> >>     
> >
> > The code for this looked good when I reviewed it earlier. I will
> > test it out with some solexa reads from here this week; any reason
> > not to check the patch and files into CVS? Then I can fire up my
> > coal-powered revision control system, feed two punch cards into the
> > mouth of the machine, hope the vacuum tubes don't burn out again,
> > and check it out locally.
> >
> > Brad
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
> >   

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