[Biopython-dev] Sequential SFF IO

Kevin Jacobs <jacobs@bioinformed.com> bioinformed at gmail.com
Wed Jan 26 23:24:51 UTC 2011

On Wed, Jan 26, 2011 at 2:44 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> I've got a better feel for what you are attempting to do now. I think
> one avenue would be to extend the write_header method to take some SFF
> specific arguments and add a write_footer method taking the optional
> Roche XML manifest which would (assuming it could seek) write the
> index block and update the header. All this may not make much sense
> without looking at the code and the SFF format spec.
This is essentially what I'm doing.  The index and manifest are written
after the flow records, so this approach is quite feasible.

> I'm currently looking at trimming 5' and 3' PCR  primer sequences -
> which could equally be used for barcodes etc. I'd probably wrap this
> as a Galaxy tool (using Biopython).
I have 90% of such a tool written.  I use a banded Smith-Waterman alignment
to match barcodes and generic PCR adapters/consensus sequence to ensure that
adapters and barcodes can be detected at both ends of reads.


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