How to use the cellbrowser.readGeneSymbols function in cellbrowser

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github maximilianh / cellBrowser / src / cbPyLib / cellbrowser / hubmaker.py View on Github external
if geneType.startswith("symbol"):
        # create a mapping from symbol -> gene locations
        if "/" in geneType:
            defGenes = geneType.split("/")[1]
        elif genome=="hg38":
            defGenes = "gencode24"
        elif genome=="hg19":
            defGenes = "gencode19"
        elif genome=="mm10":
            defGenes = "gencode-m13"
        else:
            errAbort("Unclear how to map symbols to genome for db %s. Please adapt cellbrowser.py" % genome)

        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
github maximilianh / cellBrowser / src / cbPyLib / cellbrowser / hubmaker.py View on Github external
defGenes = "gencode19"
        elif genome=="mm10":
            defGenes = "gencode-m13"
        else:
            errAbort("Unclear how to map symbols to genome for db %s. Please adapt cellbrowser.py" % genome)

        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