/usr/share/pyshared/Epigrass/spread.py is in epigrass 2.3.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#spread display and analisys
#
#try:
# from PyQt4.QtGui import *
#except ImportError:
# print "Please install PyQT 4"
#from qt import *
from xml.dom import minidom, Node
import os, json
from numpy import *
import networkx as nx
from networkx.readwrite import json_graph
import codecs
class Spread:
def __init__(self, graphobj, outdir='.',encoding='utf-8'):
self.g = graphobj
self.nxg = nx.MultiDiGraph()
self.outdir = outdir
self.encoding = encoding
self.create_tree()
nx.write_graphml(self.nxg,os.path.join(outdir,'spread.graphml'),encoding=encoding)
nx.write_gml(self.nxg,os.path.join(outdir,'spread.gml'))
nl = json_graph.node_link_data(self.nxg)
with open(os.path.join(outdir,'spread.json'),'w') as f:
json.dump(nl,f)
# nx.write_dot(self.nxg,os.path.join(outdir,'spread.graphml'))
# graphml = GraphML(self.g, outdir, encoding)
# graphml.write()
def create_tree(self):
"""
Generates a unambiguous spread tree by selecting the most likely infector for each site
"""
#Creating nodes and edges
for n in self.g.epipath:
infected = self.g.site_dict[n[1]]
infectors = n[-1]
self.nxg.add_node(n[1],name=infected.sitename,time=n[0])
for i, c in infectors.iteritems():
self.nxg.add_edge(n[1],i.geocode,weight=float(c))
def writeGML(self,tree, outdir,encoding,fname="spreadtree.gml"):
"""
Save the tree in the GML format
"""
try:
os.chdir(outdir)
except:
pass
dir(self)
f = codecs.open(fname,'w', encoding)
f.writelines(['Creator "Epigrass"\n',
'Version ""\n',
'graph\n[\n',
'\thierarchic\t1\n'
'\tlabel\t"Spread Tree"\n'
'\tdirected\t1\n'])
#self.writeENGML(f,tree)
Spread.writeENGML(f,tree) #calling as a class method
f.write(']')
f.close()
print "Wrote %s"%fname
writeGML = classmethod(writeGML)
def writeENGML(self,fobj,tree):
"""
Write the edges and Nodes section of a GML file
"""
f=fobj
#Create dictionary of node IDs, and eliminate possible node duplicates.
nodes = dict([(i[1],n) for n,i in enumerate(tree)])
for n,k in enumerate(nodes.iterkeys()):
nodes[k] = n
#writing nodes
for i,n in nodes.iteritems():
f.writelines(['\tnode\n','\t[\n'])
f.writelines(['\t\tid\t%s\n'%n,'\t\tlabel\t"%s"\n'%i])
f.writelines(['\t\tgraphics\n','\t\t[\n','\t\t\tw\t60\n','\t\t\th\t30\n'])
f.writelines(['\t\t\ttype\t"roundrectangle"\n','\t\t\tfill\t"#FFCC00"\n','\t\t\toutline\t"#000000"\n','\t\t]\n'])
f.writelines(['\t\tLabelGraphics\n','\t\t[\n','\t\t\ttext\t"%s"\n'%i,'\t\t\tfontSize\t13\n','\t\t\tfontName\t"Dialog"\n','\t\t\tanchor\t"c"\n','\t\t]\n','\t]\n'])
#writing Edges
for n,i in enumerate(tree):
lab = str(i[0])
tid = nodes[i[1]]
try: #If the source is NA (seed site)
sid = nodes[i[2]]
except KeyError:
continue
#print lab
f.writelines(['\tedge\n','\t[\n'])
f.writelines(['\t\tsource\t%s\n'%sid,'\t\ttarget\t%s\n'%tid,'\t\tlabel\t"%s"\n'%lab,'\t\tgraphics\n','\t\t[\n'])
f.writelines(['\t\t\tfill\t"#000000"\n','\t\t\ttargetArrow\t"standard"\n','\t\t]\n','\t]\n'])
writeENGML = classmethod(writeENGML)
#class GraphML:
# def __init__(self,graphobj, outdir, encoding,fname="spread.graphml" ):
# """
# Generates a valid GraphML document from the spread tree.
# """
# self.g = graphobj
# self.encoding = encoding
# self.outdir = outdir
# self.fname = fname
# self.doc = minidom.Document()
# # Creating Root element
# gml = self.doc.createElement("graphml")
# gml.setAttribute("xmlns","http://graphml.graphdrawing.org/xmlns")
# gml.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance")
# gml.setAttribute("xsi:schemaLocation", "http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd")
# self.addAttrKeys(gml)
#
# # Creating graph Element
# self.gr = self.doc.createElement("graph")
# self.gr.setAttribute("id", "graphname")
# self.gr.setAttribute("edgedefault", "directed")
#
# #Creating nodes and edges
# self.nodes = []
# for n in self.g.epipath:
# infected = self.g.site_dict[n[1]]
# infectors = n[-1]
# self.addNodeEl(n[1], infected.sitename)
# self.nodes.append(n[1])
# for i, c in infectors.iteritems():
# self.addNodeEl(i.geocode, i.sitename)
# self.addEdgeEl(i.geocode, n[1], n[0], c)
# gml.appendChild(self.gr)
# self.doc.appendChild(gml)
#
# def addNodeEl(self, gc , name):
# """
# Adds a Node element to the Graphml object
# """
# if gc in self.nodes:
# return
# else:
## print gc, name
# nd = self.doc.createElement("node")
# nd.setAttribute("id", "n"+str(gc))
# data = self.doc.createElement("data")
# data.setAttribute("key", "d0")
# data.appendChild(self.doc.createTextNode(name))
# nd.appendChild(data)
# self.gr.appendChild(nd)
#
# def addEdgeEl(self, s, d , t, ino):
## print s, d , t , ino
# ed = self.doc.createElement("edge")
# ed.setAttribute("source", str(s))
# ed.setAttribute("target", str(d))
# data = self.doc.createElement("data")
# data.setAttribute("key", "d1")
# data.appendChild(self.doc.createTextNode(str(ino)))
# ed.appendChild(data)
# data = self.doc.createElement("data")
# data.setAttribute("key", "d2")
# data.appendChild(self.doc.createTextNode(str(t)))
# ed.appendChild(data)
# self.gr.appendChild(ed)
#
# def addAttrKeys(self, gml):
# k1 = self.doc.createElement("key")
# k1.setAttribute("id", "d0")
# k1.setAttribute("for", "node")
# k1.setAttribute("attr.name", "label")
# k1.setAttribute("attr.type", "string")
# gml.appendChild(k1)
# k2 = self.doc.createElement("key")
# k2.setAttribute("id", "d1")
# k2.setAttribute("for", "edge")
# k2.setAttribute("attr.name", "Innoculum")
# k2.setAttribute("attr.type", "int")
# gml.appendChild(k2)
# k3 = self.doc.createElement("key")
# k3.setAttribute("id", "d2")
# k3.setAttribute("for", "edge")
# k3.setAttribute("attr.name", "timestep")
# k3.setAttribute("attr.type", "int")
# gml.appendChild(k3)
# def write(self):
# """
# Writes the graphml file to disk
# """
# fullpath = os.path.join(self.outdir,self.fname)
# f=open(fullpath,"w")
## f.write('<?xml version="1.0" encoding="%s"?>'%self.encoding)
# f.write(self.doc.toprettyxml(encoding=self.encoding))
# f.close()
#
#class Consensus:
# def __init__(self,path,cutoff=0.0):
# tl = self.readTress(path)
# self.consensus(tl,cutoff)
# def readTress(self,path):
# """
# Read all files named epipath* from the current dir
# and return a collection of trees.
# """
# if not os.path.exists(path+'epipath.csv'):
# print "No tree files available on this path"
# else:
# f = open(path+'epipath.csv','r')
# treelist = [self.parseEpipath(f.readlines())]
# f.close()
# n=1
# fname = path+'epipath'+str(n)+'.csv'
# while os.path.exists(fname):
# f= open(fname, 'r')
# print "Reading %s ..." % fname
# treelist.append(self.parseEpipath(f.readlines()))
# f.close()
# n+=1
# fname = path+'epipath'+str(n)+'.csv'
# return treelist
#
#
# def parseEpipath(self,lines):
# """
# Receives a list of strings and returns a list of tuples
# """
# tree = [tuple(l[:-1].split(',')) for l in lines]
# return tree
#
#
# def consensus(self, treelist, cutoff):
# """
# Generate a consensus tree from the various trees generated by multiple runs.
# Saves the tree in gml format file
# """
# cons = {}
# trees = []
# for t in treelist:
# trees += t #concatenate all the trees
### import tree
### cons = tree.tree(trees)
# #print len(trees)
# for i in trees[1:]:
# try:
# cons[i[1]+'-'+i[2]] += 1
# except:
# try:
# cons[i[2]+'-'+i[1]] += 1
# except:
# cons[i[1]+'-'+i[2]] = 1
# #print len(cons)
#
# maxsup = max(cons.values())
# const = [tuple([v]+k.split('-')) for k,v in cons.items()if float(v)/maxsup > cutoff[0]/100.]
# Spread.writeGML(const,'.','latin-1','consensus_tree.gml')
#
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