[Biopython-dev] Bio.SeqIO.convert function?

[Peter]

On Mon, Aug 10, 2009 at 5:46 PM, Peter<biopython at maubp.freeserve.co.uk> wrote:
> On Sat, Aug 8, 2009 at 12:14 PM, Peter<biopython at maubp.freeserve.co.uk> wrote:
>> I've stuck a branch up on github which (thus far) simply defines
>> the Bio.SeqIO.convert and Bio.AlignIO.convert functions.
>> Adding optimised code can come later.
>>
>> http://github.com/peterjc/biopython/commits/convert
>
> There is now a new file Bio/SeqIO/_convert.py on this
> branch, and a few optimised conversions have been done.
> In particular GenBank/EMBL to FASTA, any FASTQ to
> FASTA, and inter-conversion between any of the three
> FASTQ formats.
>
> The current Bio/SeqIO/_convert.py file actually looks very
> long and complicated - but if you ignore the doctests (which
> I would probably move to a dedicated unit test), it isn't that
> much code at all.

I have now moved all the test code to a new unit test file,
test_SeqIO_convert.py, and think this code is ready for public
testing/review, with a the aim of inclusion in Biopython 1.52
(i.e. it can wait until after 1.51 is done). I would still need
to add this to the tutorial, but that won't take very long.

Peter