[Biopython-dev] Sequential SFF IO

[Kevin Jacobs <jacobs@bioinformed.com>]

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.

-Kevin