def main():
(spec, odict) = parseOrthoFile( sys.argv[1] )
recDir = sys.argv[2]
ofname = sys.argv[3]
orthoGroups = odict.keys()
with open(ofname,'wb') as ofile:
for og in orthoGroups:
ifname = "{0}/{1}.nwk.rooting.0".format(recDir,og)
t = cogent.LoadTree(ifname)
ofile.write(t.Name+"\n")
sys.exit(1)
def main():
(spec, odict) = parseOrthoFile(sys.argv[1])
recDir = sys.argv[2]
ofname = sys.argv[3]
orthoGroups = odict.keys()
with open(ofname, 'wb') as ofile:
for og in orthoGroups:
ifname = "{0}/{1}.nwk.rooting.0".format(recDir, og)
t = cogent.LoadTree(ifname)
ofile.write(t.Name + "\n")
sys.exit(1)
def main(args):
usingParana = (args["--method"].upper() == "PARANA")
usingRWS = (args["--method"].upper() == "RWS")
outputCVFile = (args["--method"].upper() == "CV")
(spec, odict) = parseOrthoFile( args["--ortho"] ) #sys.argv[1] )
recDir = args["--recdir"]#sys.argv[2]
ofname = args["--outdir"]#sys.argv[3]
beta = float(args["--beta"])
if not outputCVFile:
mkdir_p(ofname)
getName = lambda x : x.Name
def getRelevantEdges( adjGraph, t1, t2 ):
pxml = Phyloxml()
pxml.build_from_file(t1)
pxml.build_from_file(t2)
la = filter( lambda x : x.find('LOST') == -1, pxml.phylogeny[0].get_leaf_names() )
lb = filter( lambda x : x.find('LOST') == -1, pxml.phylogeny[1].get_leaf_names() )
#lb = filter( lambda x : x.find('LOST') == -1, map( getName, cogent.LoadTree(t2).tips() ) )
crossValidationEdges = filter( lambda (x,y) : ((x in la) and (y in lb)) or ((y in la) and (x in lb)) , adjGraph.edges() )
relevantEdges = filter( lambda (x,y) : ((x in la) or (x in lb)) and ((y in la) or (y in lb)) , adjGraph.edges() )
newGraph = nx.Graph()
newGraph.add_nodes_from( la + lb )
newGraph.add_edges_from( relevantEdges )
return newGraph, crossValidationEdges
if outputCVFile:
root = ET.Element("cvtest", name="herpes_loocv")
ctr = 0
orthoGroups = odict.keys()
progress = ProgressBar(len(orthoGroups)*len(orthoGroups)).start()
for i, (og1, og2) in enumerate(iterWithSelf(orthoGroups)):
progress.update(i)
#print("computing ancestral state between groups {0} and {1}".format(og1, og2))
#print("i = {0}".format(i))
alist = nx.read_adjlist(extantName)
t1name = "{0}/{1}.xml.rooting.0.ntg.reconciled.0.ntg.rearrange.0.ntg".format(recDir,og1)
t2name = "{0}/{1}.xml.rooting.0.ntg.reconciled.0.ntg.rearrange.0.ntg".format(recDir,og2)
relevantGraph, crossValidationEdges = getRelevantEdges(alist, t1name, t2name)
if len(crossValidationEdges) > 1:
for e in crossValidationEdges:
cGraph = relevantGraph.copy()
cGraph.remove_edge(e[0], e[1])
ofileName = "{0}/{1}@{2}@removed@{3}#{4}@txt".format(ofname, og1, og2, e[0], e[1])
assert(cGraph.size() == relevantGraph.size()-1)
callargs = None
if usingParana:
with tempfile.NamedTemporaryFile(mode='wb', suffix='.adj', prefix='tmp', dir="/tmp", delete=True) as gfile:
nx.write_adjlist(cGraph, gfile.name)
callargs = constructParanaCall(gfile, ofileName, beta, og1, og2, t1name, t2name)
os.system(" ".join(callargs)+"> /dev/null 2>&1")
elif usingRWS:
copy = alist.copy()
copy.remove_edge(e[0],e[1])
#print(cGraph.size())
runRWS(copy, ofileName)
elif outputCVFile:
tset = ET.SubElement(root, "testset", name="fold_{0}".format(ctr))
u,v = sorted((e[0],e[1]))
ET.SubElement(tset, "edge", u=u, v=v)
ctr += 1
else:
raise "Method must be one of {Parana|RWS}"
#p = subprocess.Popen( callargs , shell=True, stdin=subprocess.PIPE, stderr=subprocess.PIPE )
#out, err = p.communicate()
if outputCVFile:
with open(ofname,'wb') as ofile:
ofile.write(ET.tostring(root, pretty_print=True))
progress.finish()
sys.exit(1)
