[BioPython] Reading Roche 454 binary SFF files in Python

[Peter]

On Wed, Apr 15, 2009 at 10:01 AM, Jose Blanca <jblanca at btc.upv.es> wrote:
>> > The main problem would be to have sff files small enough to be used
>> > for the test.
>>
>> The Roche command line tools allow you to take a large SFF file and
>> produce a filtered version (use sfffile with the -i option and a simple
>> text file of read identifiers).  So making a small SFF file for unit tests
>> should be simple.
>
> Could you send a couple of example sff files to me?
>

I'm not sure what SFF data I would be allowed to distribute, especially if
you want it for a publicly available unit test example.  Once the analysis
is published, I'm sure this would be easier, but there would still be some
administrative channels at work to go though to do this officially.

It might be simpler if you gave me the URL of a public SFF file (or one
of your own files) you would like split up, and I make a reduced version
of that.  Email me off list and we can talk about this.

> I haven't the Roche tools, that's why I implemented sff_extract in the
> first place :)

Try have a word with the sequencing center where you get your Roche
454 sequencing done - they may be able to organize access to the
software for you with Roche's approval.  That's what we did.

Peter