[Biopython-dev] sff file

[Sebastian Bassi]

On Tue, Oct 27, 2009 at 8:50 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> As part of the polishing in anticipation of merging the SFF support
> into the trunk, I've just made some big additions to the docstring
> (with doctest examples) on the branch - it would be great if you
> could read over this at some point.
> http://github.com/peterjc/biopython/tree/sff-seqio

I've read it (you mean the code in SffIO.py). Regarding your questions:

> What do you think of the current rather pragmatic way I'm
> handling trimming the SeqRecord objects? i.e. SeqIO file format
> "sff" gives the full data and supports reading and writing, while
> SeqIO format "sff-trim" only supports reading and gives trimmed
> sequences without the flow data. This is a bit of a hack, and the
> "sff-trim" format could be left out - but then we would need a nice
> way to trim the full length SeqRecord objects...

sff-trim is OK for me but I am not familiar with this format. I see
there are some mixed upper and lower case dna sequence, why? Are lower
case bases with less quality? (like the both extremes in standards
read).