How to use the cellbrowser.getSizesFname function in cellbrowser

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github maximilianh / cellBrowser / src / cbPyLib / cellbrowser / hubmaker.py View on Github external
bedFh.write("\n")

    bedFh.close()

    if skipCount != 0:
        logging.info("Could not place %d genes, these were skipped" % skipCount)

    bedFname2 = bedFname.replace(".bed", ".sorted.bed")
    cmd = "LC_COLLATE=C sort -k1,1 -k2,2n %s > %s" % (bedFname, bedFname2)
    cellbrowser.runCommand(cmd)

    # convert to .bb using .as file
    # from https://genome.ucsc.edu/goldenpath/help/examples/barChart/barChartBed.as
    #asFname = join(dataDir, )
    asFname = cellbrowser.getStaticFile(["genomes", "barChartBed.as"])
    sizesFname = cellbrowser.getSizesFname(genome)

    cmd = "bedToBigBed -as=%s -type=bed6+5 -tab %s %s %s" % (asFname, bedFname2, sizesFname, bbFname)
    cellbrowser.runCommand(cmd)
github maximilianh / cellBrowser / src / cbPyLib / cellbrowser / hubmaker.py View on Github external
idReportFname = join(outDir, "metaBamMatch.txt")
    cellCount = writeDebugReport(allMetaCellIds, cellIdToBams, clusterBams, idReportFname)

    jlFh = open("jobList", "w")

    #cellCount = 0
    for clusterName, (cellIds, bamFnames) in clusterBams.iteritems():
        uniqueCellIds = set(cellIds)
        #cellCount += len(uniqueCellIds)

    logging.info("Merging BAM files and writing hub")
    saneHubName = sanitizeName(hubName)
    writeParentStanzas(tfh, saneHubName, hubName, cellCount)

    chromSizes = cellbrowser.getSizesFname(db)

    jobNo = 0
    emptyClusterCount = 0
    for clusterName, (cellIds, bamFnames) in clusterBams.iteritems():
        saneClusterName = sanitizeName(clusterName)
        logging.info("Processing cluster %s, %d cellIds/BAM files, examples: %s" % (clusterName, len(cellIds), cellIds[0]))
        cmds = []

        outBam = join(outDir, saneClusterName+".bam")
        outStat = join(outDir, saneClusterName+".stats.txt")
        outCalls = join(outDir, saneClusterName+".calls.tsv")
        junctionBed = join(outDir, saneClusterName+".junctions.bed")
        intronBed = join(outDir, saneClusterName+".introns.bed")

        junctionBedSorted = junctionBed.replace(".bed", ".sorted.bed")
        intronBedSorted = intronBed.replace(".bed", ".sorted.bed")