[Biopython] Bio.Phylo AttributeError: 'module' object has no attribute 'draw'

[Eric Talevich]

On Fri, Mar 2, 2012 at 8:48 AM, Mariam Reyad Rizkallah <mrrizkalla at gmail.com
> wrote:

> >
> > Dear Biopython list,
> >
> > I am facing similar problem with Phylo in the context of your thread. I
> am
> > using Biopython 1.58 - Ubuntu 32 bit system. I have created a newick
> using
> > phyml command-line and want to visualize it using Bio.Phylo. I read the
> > newick, draw_ascii and draw_graphiz perfectly but not draw(). I have
> > networkx, and pylab installed.
> >
> > my_view_tree = Phylo.read("myseq.phy_phyml_tree.txt", "newick")
> > Phylo.draw_ascii(my_view_tree)
> > my_view_tree_xml = my_view_tree.as_phyloxml()
> > Phylo.draw(my_view_tree_xml, do_show=True, show_confidence=True,
> axes=None)
> >
> > *Error:*
> >
> > Traceback (most recent call last):
> >   File "itree/itree2/iTree2.py", line 563, in view_tree
> >     Phylo.draw(my_view_tree_xml, do_show=True, show_confidence=True,
> > axes=None)
> > AttributeError: 'module' object has no attribute 'draw'
> >
> >
> Thank you.
>
> Mariam
>
>
Hi Mariam,

Would you mind checking the version number of Biopython within the
interpreter or script you're using? Like this:

import Bio
print Bio.__version__


The function Phylo.draw was part of Biopython 1.58, so the simplest
explanation is that your script is using a different, older installation of
Biopython that's also installed on your system.

Alternatively, to get the best experience with Phylo.draw I'd recommend
updating to the current Biopython 1.59.

Hope that helps,
Eric