[Biopython-dev] Next release plans?

Peter biopython at maubp.freeserve.co.uk
Mon Jul 27 16:18:11 UTC 2009

On Thu, Jul 23, 2009 at 12:08 PM, Peter<biopython at maubp.freeserve.co.uk> wrote:
> The FASTQ checking is on going. I have updated our FASTQ
> code to map Solexa scores as I understood Peter Rice's
> description of the intended EMBOSS behaviour (this is for the
> corner case of very poor quality reads). However, due to a
> couple of minor bugs I found in EMBOSS 6.1.0 we'll either
> have to cross check against their CVS code, or hope they
> release EMBOSS 6.1.1 soon.
> Cross checking against MAQ would also be worthwhile, but
> while there are some patches about to fix a couple of MAQ
> FASTQ bugs and include Illumina to Sanger standard
> conversion, this isn't in their official repository yet.
> I guess I could cross check against BioPerl's new FASTQ
> support ...

The FASTQ cross-validation is on going, as you may have
gathered from the cross-project thread (now on open-bio-l)
I did start testing against BioPerl SVN which uncovered
some BioPerl problems, and a grey area of the format
worth debate. See also:

This is taking longer than I had expected, but think it will be
worth the effort.


P.S. Anyone care to guess on how EMBOSS, BioPerl, and
Biopython's FASTQ parsing stacks up in terms of run time?

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