[Biopython-dev] Biopython 1.60 plans and beyond

[Michiel de Hoon]

--- On Sat, 2/18/12, Tiago Antão <tiagoantao at gmail.com> wrote:
> Another side issue that I would like to discuss (maybe a
> different
> thread): Is how people are coping with large amounts of data
> using
> Python (or Perl/Ruby for that matter)? Specifically the
> problem of
> performance. As I see it, there is more and more the case of
> depending
> on external (fast) programs or CLib extensions or Java
> extensions to
> do the bulk of the work. Inner-loops in Python simply do not
> cut for speed.

C extensions to Python such as pysam, together with outer-loops in Python/Biopython have been working very well for me. Perhaps at some point pysam can be included into Biopython, but as samtools is still evolving it makes sense for it to be a separate package so that it can be updated more quickly.

I am more concerned about relying on external programs, in particular R. Notwithstanding the usefulness of rpy and rpy2, I would prefer to have a pure-Python or Python-with-C-extension solution, ideally as part of Biopython.

-Michiel.