[Bioperl-l] Announcing Bio::SFF

[Leon Timmermans]

On Wed, Dec 14, 2011 at 5:03 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Hi Leon,
>
> Have you looked at the index block at all, in order to offer random
> access by read ID, or to access the Roche XML manifest? Please
> ask if you need more information about this - or if you can read Python:
> https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py
>

I have looked at it, but not implemented it yet. There is no standardized
index, and the ones that are in common use either seem stupid (the Roche
index, which is essentially just a weirdly formatted sequential list,
though that should still be faster than a table scan) or undocumented (hash
based index).

 Is this building on Miguel Pignatelli's work? I don't recall seeing
> any follow up posts from him after this one:
> http://lists.open-bio.org/pipermail/bioperl-l/2010-November/034239.html
>

It isn't. I like his idea for reusing BioPython's test files though.

Leon