How to use the cellbrowser.MatrixTsvReader function in cellbrowser

logging.info("Using %s to map symbols to genome" % defGenes)

        geneToSym = cellbrowser.readGeneSymbols({'geneIdType':defGenes})
        geneLocsId = cellbrowser.parseGeneLocs(defGenes)
        geneLocs = {}
        for geneId, locs in iterItems(geneLocsId):
            sym = geneToSym[geneId]
            geneLocs[sym] = locs
    else:
        geneToSym = cellbrowser.readGeneSymbols({'geneIdType':geneType})
        geneLocs = cellbrowser.parseGeneLocs(geneType)

    matOfh = open(outMatrixFname, "w")
    clustOfh = open(clusterFname, "w")

    mr = cellbrowser.MatrixTsvReader()
    mr.open(inMatrixFname)
    matType, cellNames = mr.matType, mr.sampleNames

    cellIds = range(0, len(cellNames))
    cellNameToId = dict(zip(cellNames, cellIds))

    # make a list of lists of cellIds, one per cluster, in the right order
    clusterCellIds = [] # list of tuples with cell-indexes, one per cluster
    allCellNames = [] # list for cellIds, with a matrix, meta and with bam file
    allCellIndices = [] # position of all cellIds in allCellNames
    for clusterName in clusterOrder:
        cellIdxList = []
        for cellName in clusterToCells[clusterName]:
            if cellName not in cellNameToId:
                logging.warn("%s is in meta but not in expression matrix." % cellName)
                continue