#9010: Upgrade biopython package to 1.54
---------------------------------+------------------------------------------
Reporter: mhampton | Owner: tbd
Type: enhancement | Status: new
Priority: major | Milestone: sage-4.4.3
Component: optional packages | Keywords:
Author: | Upstream: N/A
Reviewer: | Merged:
Work_issues: |
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Comment(by awebb):
I tried the new Phylo module and it is nice. I had a problem with one
example with networkx. (files in Tests/PhyloXML)
{{{
sage: from Bio import Phylo
sage: import networkx, pylab
sage: tree = Phylo.read('example.xml', 'phyloxml')
sage: net = Phylo.to_networkx(tree)
sage: networkx.draw(net)
TypeError Traceback (most recent call
last)
/home/adamwebb/download/biopython-1.54.p0/src/Tests/PhyloXML/<ipython
console> in <module>()
/home/math/sage/local/lib/python/networkx/drawing/nx_pylab.pyc in draw(G,
pos, ax, hold, **kwds)
108
109 if pos is None:
--> 110 pos=networkx.drawing.spring_layout(G) # default to spring
layout
111
112 cf=pylab.gcf()
/home/math/sage/local/lib/python/networkx/drawing/layout.pyc in
fruchterman_reingold_layout(G, dim, pos, fixed, iterations, weighted,
scale)
209 weighted=weighted)
210 except:
--> 211 A=networkx.to_numpy_matrix(G)
212 pos=_fruchterman_reingold(A,
213 pos=pos_arr,
/home/math/sage/local/lib/python/networkx/convert.pyc in
to_numpy_matrix(G, nodelist, dtype, order)
478 if (u in nodeset) and (v in nodeset):
479 i,j = index[u],index[v]
--> 480 M[i,j] += attrs.get('weight', 1)
481 if undirected:
482 M[j,i] = M[i,j]
TypeError: unsupported operand type(s) for +=: 'numpy.float64' and 'str'
}}}
The next line would be.
sage: pylab.show()
I installed pygraphviz as well and the other graphing examples worked.
Adam
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/9010#comment:3>
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