[Biopython] Bio.SeqIO.index() - gzip support and/or index stored on disk?

[Kevin Lam]

>
> Tokyocabinet is certainly an interesting project, but this isn't the issue
> that Bio.SeqIO.index() is trying to solve. You might be interested in
> Brad's blog post from last year:
>
>
> http://bcbio.wordpress.com/2009/05/10/evaluating-key-value-and-document-stores-for-short-read-data/
>
> Regards,
>
> Peter
>


> Hi Peter
> Can I summarise it? I think alot of well meaning ppl are pushing for their
> fav db but
>


>  using a disk based db like sqlite for Bio.SeqIO.index() for recording the
> file offset is going to be the best way to do it versus trying to find
> another suitable non-mysql db variant to 'databasify' the short read-data?
> As the latter would be relatively easy for anyone else interested to
> experiment to code their own scripts for their fav db
>
> :)

>
>
> this post on this mongodb is interesing btw.
> http://blog.zawodny.com/2010/05/22/mongodb-early-impressions/
>
>