#A.append(StrListToFloatList(selectListByIndexVector(fields,grp1Selector))) #B.append(StrListToFloatList(selectListByIndexVector(fields,grp2Selector))) for groupDataMatrix,groupLabelSelector in zip(groupData,groupLabelSelectors): groupLabel,groupSelectors=groupLabelSelector groupDataMatrix.append(StrListToFloatList(selectListByIndexVector(fields,groupSelectors))) fil.close() #now transpose #A=matrix_transpose(A,len(A),len(A[0]))[0] #get the data only, discards the nrow and ncol #B=matrix_transpose(B,len(B),len(B[0]))[0] for i in range(0,len(groupData)): groupData[i]=matrix_transpose(groupData[i],len(groupData[i]),len(groupData[i][0]))[0] #now calculate distance #dist=linkage(A,B,method) for i in range(0,len(groupLabelSelectors)): for j in range(i,len(groupLabelSelectors)): ALabel=groupLabelSelectors[i][0] BLabel=groupLabelSelectors[j][0] if i==j: print >> stdout,"%s\t%s\t%f" %(ALabel,BLabel,0.0) continue A=groupData[i]
#A.append(StrListToFloatList(selectListByIndexVector(fields,grp1Selector)))
#B.append(StrListToFloatList(selectListByIndexVector(fields,grp2Selector)))
for groupDataMatrix, groupLabelSelector in zip(groupData,
groupLabelSelectors):
groupLabel, groupSelectors = groupLabelSelector
groupDataMatrix.append(
StrListToFloatList(
selectListByIndexVector(fields, groupSelectors)))
fil.close()
#now transpose
#A=matrix_transpose(A,len(A),len(A[0]))[0] #get the data only, discards the nrow and ncol
#B=matrix_transpose(B,len(B),len(B[0]))[0]
for i in range(0, len(groupData)):
groupData[i] = matrix_transpose(groupData[i], len(groupData[i]),
len(groupData[i][0]))[0]
#now calculate distance
#dist=linkage(A,B,method)
for i in range(0, len(groupLabelSelectors)):
for j in range(i, len(groupLabelSelectors)):
ALabel = groupLabelSelectors[i][0]
BLabel = groupLabelSelectors[j][0]
if i == j:
print >> stdout, "%s\t%s\t%f" % (ALabel, BLabel, 0.0)
continue
A = groupData[i]
B = groupData[j]
#two pass
fil=open(filename)
lino=0
for lin in fil:
lino+=1
if lino<startRow:
continue
fields=lin.rstrip("\r\n").split(fs)
Matrix.append(toFloatList(getSubvector(fields,cols)))
fil.close()
#now Matrix is gotten, quantile normalize
Matrix,MtRow,MtCol=matrix_transpose(Matrix,len(Matrix),len(Matrix[0]))
quantileNormalizeMInPlace(Matrix,method)
Matrix,MtRow,MtCol=matrix_transpose(Matrix,MtRow,MtCol)
#print >> stderr,Matrix
#now second pass
fil=open(filename)
lino=0
for lin in fil:
lino+=1
fields=lin.rstrip("\r\n").split(fs)
if lino<startRow:
pass
else:
fillVectorByIndexAsString(fields,Matrix[lino-startRow],cols)
#two pass
fil = open(filename)
lino = 0
for lin in fil:
lino += 1
if lino < startRow:
continue
fields = lin.rstrip("\r\n").split(fs)
Matrix.append(toFloatList(getSubvector(fields, cols)))
fil.close()
#now Matrix is gotten, quantile normalize
Matrix, MtRow, MtCol = matrix_transpose(Matrix, len(Matrix),
len(Matrix[0]))
quantileNormalizeMInPlace(Matrix, method)
Matrix, MtRow, MtCol = matrix_transpose(Matrix, MtRow, MtCol)
#print >> stderr,Matrix
#now second pass
fil = open(filename)
lino = 0
for lin in fil:
lino += 1
fields = lin.rstrip("\r\n").split(fs)
if lino < startRow:
pass
else:
fillVectorByIndexAsString(fields, Matrix[lino - startRow], cols)