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

Peter biopython at maubp.freeserve.co.uk
Mon Nov 23 09:43:28 EST 2009

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:

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):

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.



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