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

[Peter]

On Mon, Mar 16, 2009 at 12:16 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Bug 2767 - Bio.SeqIO support for FASTQ and QUAL files

That's in CVS now, Brad and I have used it a bit, but further testing
before the beta wouldn't hurt.

> Bug 2551 - Adding advanced __getitem__ to generic alignment, e.g.
> align[1:2,5:-5]

Anyone want try this out?
http://bugzilla.open-bio.org/show_bug.cgi?id=2551

> Any other nominations for Biopython 1.50?

Other candidates with patches that have since come to mind:

Bug 2733 - Runing unit tests where Biopthyon wasn't built from source
http://bugzilla.open-bio.org/show_bug.cgi?id=2733
This seemed patch seemed OK from both my and Bruce's testing.

Bug 2738 - Speed up GenBank parsing, in particular location parsing
http://bugzilla.open-bio.org/show_bug.cgi?id=2738
I would want to run some theses with EMBL files before committing this.

Bug 2745 - Bio.GenBank.LocationParserError with a GenBank CON file
http://bugzilla.open-bio.org/show_bug.cgi?id=2745
I'd like to change CONTIG line parsing to just use a string (or a list
of strings).

Peter