[Biopython] Intro

[Dragoslav Zaric]

Peter,

Thank you so very much for detailed explanations.

I will try to upgrade biopython version under linux.

Kind regards,

Dragoslav Zaric


On Tue, Sep 14, 2010 at 3:44 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> 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
>