[BioRuby] bioruby sff reader

[Peter Cock]

On Tue, Feb 15, 2011 at 4:09 PM, Francesco Strozzi
<francesco.strozzi at gmail.com> wrote:
> Hi all,
> is there a SFF reader to parse 454 output in Ruby? Or is someone working on
> this?
> It will be nice to have something like python sff-extract which can read the
> SFF format and generate ad hoc files like FastQ or Fasta, Qual and XML
> traceinfo.

If all you want to to convert SFF to FASTQ or FASTA+QUAL plus perhaps
the NCBI XML traceinfo why not just use the sff_extract.py script?

On the other hand, I can see the utlity in native support for SFF files in
(Bio)Ruby. Biopython does this already and there has been some work
towards this for BioPerl and BioJava too:

http://lists.open-bio.org/pipermail/bioperl-l/2010-November/034223.html
http://lists.open-bio.org/pipermail/biojava-dev/2010-November/004451.html

Please feel free to look at the Biopython SFF code for this. It was
originally based on sff_extract for parsing, but extended to also write
SFF and handle the (undocumented) Roche index block. I've tried
to include enough comments within the code to make it clear, but
I'll happily answer technical questions:
https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py

There are also unit test example files you can use:
https://github.com/biopython/biopython/tree/master/Tests/Roche

Peter
(Biopython)