def distanceTable(frq,method,outfile,met):
keyDict = sorted(np.unique(("/".join(frq.keys())).split("/")));
mapDict = dict()
if method == 'min':
mapDict =minDistance(frq)
elif method == 'prod':
mapDict =prodDistance(frq,met)
pr.printDistanceTableToFile(mapDict,keyDict,outfile)
def anchoredDistance(**kwargs):
readFromTable=False
for k,v in kwargs.iteritems():
if k == "qfile":
qfile=v
readFromTable = True
elif k == "achs":
achs = sorted(v)
elif k == "gt":
trees = v
elif k == "outfile":
outfile = v
elif k == "wrkPath":
out = v
elif k == "taxa":
taxa = v
if(readFromTable):
frq=tbs.readQuartetTable(qfile)
D = anchoredDistanceFromFrq(frq,achs)
else:
[D,frq] = findAnchoredDistanceTable(achs,trees,taxa,out)
keyDict = sorted(list(np.unique((" ".join(D.keys())).split(" "))));
pr.printDistanceTableToFile(D,keyDict,outfile)
return frq
print >> f, anch_temp
for achList in acSmall:
for anch in achList:
anch = sorted(list(anch))
anch_temp = "|".join(anch)
print >> f, anch_temp
f.close()
os.close(ftmp3[0])
for e in con_tree.postorder_node_iter():
if e in to_resolve:
z=listPoly.index(e)
keyDict = sorted(list(np.unique((" ".join(normalizedD[z].keys())).split(" "))))
fileDistance = "distancet-"+str(e.label)+".d"
ftmp3=tempfile.mkstemp(suffix='.d', prefix=fileDistance, dir=outpath, text=None)
pr.printDistanceTableToFile(normalizedD[z],keyDict,ftmp3[1])
print "writing distance table to "+str(ftmp3[1])
os.close(ftmp3[0])
ftmp4=tempfile.mkstemp(suffix='.nwk', prefix=fileDistance+"_fastme_tree.nwk",dir=outpath,text=None)
tstt.buildTreeFromDistanceMatrix(ftmp3[1],ftmp4[1],sumProg,sumProgOption)
os.close(ftmp4[0])
if verbose:
print "starting to resolve polytomy"
res=atbs.resolvePolytomy(ftmp4[1],e,verbose)
tstt.prune_tree_trivial_nodes(con_tree)
outfile = outpath+"/distique_distance-sum.nwk"
if verbose:
print "writing the resulting tree as: "+outfile
tstt.changeLabelsToNames(con_tree,new_labels,verbose)
con_tree.write(path=outfile,schema="newick",suppress_rooting=True,suppress_internal_node_labels=True)
print "The overall time to infer the species tree is: "
