[Biopython-dev] Merging Bio.SeqIO SFF support?

[Peter]

On Mon, Nov 23, 2009 at 2:43 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Dear all,
>
> Is there anyone on the dev mailing list willing to test the SFF
> support I've been working on for Bio.SeqIO? The code is here,
> a branch on github:
> http://github.com/peterjc/biopython/tree/sff-seqio
>
> The important files are:
> * Bio/SeqIO/SffIO.py
> * Bio/SeqIO/__init__.py (defining the new format)
> * Bio/SeqIO/_index.py (indexing SFF files)
>
> Plus unit test files:
> * Tests/run_tests.py (to run the doctests)
> * Tests/test_SeqIO_QualityIO.py
> * Tests/test_SeqIO_index.py
> * Tests/test_SeqIO.py
> * Tests/Roche/* (for unit tests)
>
> Sebastian Bassi had a look last month and his feedback has
> already helped (e.g. with error messages):
> http://lists.open-bio.org/pipermail/biopython-dev/2009-October/006903.html
>
> I have been using this code myself in real work, for example
> editing the trim points in an SFF file to take into account PCR
> primer sequences, and filtering SFF reads, checking Roche
> barcodes etc.
>
> Thanks,
>
> Peter
>

Hi all,

I didn't want to rush the SFF support into Biopython 1.53, but its been
waiting "ready" for a while now. Any objections or comments about
me merging this now?

Thanks,

Peter