[Biopython-dev] Next release plans?

Peter biopython at maubp.freeserve.co.uk
Fri Jul 10 12:38:43 UTC 2009

On Mon, Jun 22, 2009 at 6:57 PM, Peter wrote:
> Once the beta release is out, we'll resume taking small changes
> (especially for documentation additions or clarifications) with a
> view to releasing Biopython 1.51 final in July (probably the second
> week, after people get back from BOSC/ISMB).

OK, that didn't happen - too much to catch up on at work after
being away at BOSC/ISMB for a week. Also I will be on holiday
next week (graduation etc). I will have some limited internet
access. I'm thinking of doing the final release of Biopython 1.51
the following week (i.e. the week starting 20th July).

This will be after the annual EMBOSS release, and one little thing
I want to sort out before we release Biopython 1.51 is mapping
Solexa/PHRED scores in FASTQ files (specifically what to do with
a PHRED score of zero which is usually a dummy value, but taken
literally means "this read is wrong" or "worst than random"). After
discussion with Peter Rice at BOSC/ISMB 2009, I plan to follow
his plan for EMBOSS (map PHRED of zero to the lowest used
Solexa score, -5). Once the EMBOSS release is out, I can use it
for cross checking our FASTQ conversions.

Also, we have the Bio.Application.generic_run code to retire,
which basically means we label it as obsolete and update the
tutorial to use subprocess (see other thread), but this requires
cross platform testing.


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