[Biopython] Intro

[Peter]

On Tue, Sep 14, 2010 at 12:08 PM, Dragoslav Zaric
<zaricdragoslav at gmail.com> wrote:
> Dear All,
>
> I am new member and I like to send welcome greet to everyone.
>
> I have few newbie questions so please be cooperative :)
>

Hello and welcome :)

> 1. How can I see biopython version and is there connection between python
> version and biopython version ?

Biopython currently supports Python 2.4, 2.5, 2.6 and 2.7. Older versions
of Biopython may not have worked 100% on Python 2.7, but we did
previously support Python 2.3 and even older versions of Python.

There is a FAQ (frequently asked questions) section in the Tutorial for
how to determine the version of Biopython installed. Try:

import Bio
print Bio.__version__

The Tutorial for the latest release is online as PDF or HTML,
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
http://biopython.org/DIST/docs/tutorial/Tutorial.html

> 2. I have installed python 2.6 and biopython 1.55 on ubuntu 9.04
> (at least I think I did :)

Based on the problems below, I don't think it worked.

>    I have same installation on windows machine and everything works fine.
>    But for example when I want to use something like this:
>
>    from Bio import SeqIO
>    orchid_dict = SeqIO.index("d:\ls_orchid.fasta", "fasta")
>
>    Two problems happens in ubuntu environment:
>    first is that SeqIO complains that there is no index method

That does suggest you have an old version of Biopython. The index
function was added in Biopython 1.52, see:

http://biopython.open-bio.org/SRC/biopython/NEWS
http://news.open-bio.org/news/2009/09/biopython-release-152/

>    second is that everywhere I should put string location of file
>    biopython wants handle to file

Things like Bio.SeqIO will accept filenames in recent versions of
Biopython (since release 1.54), but older versions only accepted
file handles. This is discussed in an FAQ in recent versions of the
Tutorial which point to this section on handles:
http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:appendix-handles

>    The first thing I can think of is maybe I am using old version of
>    biopython, which points to question 1.

That does seem to be the problem.

> 3. Does somebody have experience with using biopython in django
> web site ?  Do I install biopython on web server or I can keep libraries
> in some folder and load them dynamically in code ?

I've used Biopython within TurboGears, but I haven't used django.
You should probably consult the django documentation for how they
recommend installing 3rd party libraries (e.g. they may recommend
using a virtual environment).

Peter