[Biopython] interactive shell to use with biopython?

[Andrew Perry]

On Tue, Apr 17, 2012 at 4:44 PM, Björn Johansson <
bjorn_johansson at bio.uminho.pt> wrote:

> Hi all,
>
> I would like to know what interactive shell might be a good
> alternative to use with biopython.
> Ideally, it should be possible to save interactive commands and save
> them to run later.
>
> Could you give me some examples of what youa are using?
>
> Thanks,
> Bjorn
>
>
You might want to check out iPython in notebook mode. I've only played with
it briefly, but it looks promising for interactive analysis, and cases
where you'd like to present the transcript to others.

'Regular' commandline iPython will also allow you to save the history with
the %save command.

See: http://ipython.org/ipython-doc/stable/interactive/htmlnotebook.html

To get an idea of how it works, see Titus Brown's demonstration:
http://www.youtube.com/watch?feature=player_detailpage&v=HaS4NXxL5Qc#t=132s

Andrew Perry

Postdoctoral Fellow
Whisstock Lab
Department of Biochemistry and Molecular Biology
Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia.
Mobile: +61 409 808 529