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 computeDistance(frq, method, percentile):
if method == 'min':
return minDistance(frq)
else:
return prodDistance(frq)
frq = atbs.findAnchoredDistanceTableOverallp(e,N,anch,taxa_list,taxa_inv, trees,taxa, outpath,debugFlag)
if e.label not in TreeList:
TreeList[e.label] = dendropy.TreeList()
if verbose:
print "computing the partial quartet table"
if readFromFile:
tbsa.findTrueAverageTableAnchoringOnDifferentSidesSmallPolytomiesOverallFromFile(frq,quartTable,anch,taxa_list,N1,N2,am,met)
else:
tbsa.findTrueAverageTableAnchoringOnDifferentSidesSmallPolytomiesOverall(frq,quartTable,anch,taxa_list,N1,N2,am,met)
if verbose:
print "The anchor "+str(count)+" out of "+str(numSmallAnchors)+" anchors has been finished!"
count += 1
if verbose:
print "computing distance table using the method: "+str(am)
Frq=atbs.anchoredDistanceFromFrqSmallPolytomies(quartTable,am,met)
D=pd.prodDistance(Frq,met)
keyDict = sorted(list(np.unique((" ".join(D.keys())).split(" "))))
fileDistance = "distancet-anchList-"+str(i)+".d"
ftmp3=tempfile.mkstemp(suffix='.d', prefix=fileDistance, dir=outpath, text=None)
pr.printDistanceTableToFile(D,keyDict,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])
tree_tmp = dendropy.Tree.get(path=ftmp4[1],schema='newick')
if e.label in TreeList:
TreeList[e.label].append(tree_tmp)
else:
TreeList[e.label] = dendropy.TreeList()
TreeList[e.label].append(tree_tmp)
