[Biopython-dev] sff reader

Peter biopython at maubp.freeserve.co.uk
Sat May 23 00:10:57 UTC 2009

On 5/23/09, Senthil Palanisami <spenthil at gmail.com> wrote:
> I have been working with SFF files for the past month, and can say it's
>  definitely frustrating working with custom binary formats.

At least in this case it is publicly documented. Have you needed to
write out (or edit) an SFF file yet? Have you used any paired end
reads in SFF format?

>  Take a look at sff_extract which is written in python. It converts sff files
>  into fasta and xml or caf files:
>  http://bioinf.comav.upv.es/sff_extract/index.html

That is what this code is based on - Jose Blanca is one of the authors
of  sff_extract.

>  You can find detailed specs of the format @
>  http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#header-global

I think you must have missed this thread last month ;)


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