Esempio n. 1
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def objListUtility_addBlockEdges(data, mb, featLen, numBins):
    """ Utility function for the MafBlock instance version of 
   libMafGffPlot.objListToBinnedWiggle()
   """
    from libMafGffPlot import objListUtility_indexToPos
    import math
    import sys
    for r in [mb.refStart, mb.refEnd]:
        if r > featLen:
            sys.stderr.write(
                'libMafGffPlot.py: Error in block edge step, a position is '
                'greater than the feature length, %d > %d.\n' % (r, featLen))
            sys.exit(1)

        p = objListUtility_indexToPos(r, featLen, numBins)
        if p < 0:
            sys.stderr.write(
                'libMafGffPlot.py: Error in block edge step, a position, %d, is less than 0\n'
                % p)
        elif p >= len(data['blockEdgeCount']):
            sys.stderr.write(
                'a position, %d, is greater than or '
                'equal to len(data[\'blockEdgeCount\']) %d [%d-%d]\n' %
                (p, len(data['blockEdgeCount']), mb.refStart, mb.refEnd))
        data['blockEdgeCount'][p] += 1.0
        if data['blockEdgeCount'][p] > data['blockEdgeMax']:
            data['blockEdgeMax'] = data['blockEdgeCount'][p]
Esempio n. 2
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def objListUtility_addBlockEdges(data, mb, featLen, numBins):
    """ Utility function for the MafBlock instance version of 
   libMafGffPlot.objListToBinnedWiggle()
   """
    from libMafGffPlot import objListUtility_indexToPos
    import math
    import sys

    for r in [mb.refStart, mb.refEnd]:
        if r > featLen:
            sys.stderr.write(
                "libMafGffPlot.py: Error in block edge step, a position is "
                "greater than the feature length, %d > %d.\n" % (r, featLen)
            )
            sys.exit(1)

        p = objListUtility_indexToPos(r, featLen, numBins)
        if p < 0:
            sys.stderr.write("libMafGffPlot.py: Error in block edge step, a position, %d, is less than 0\n" % p)
        elif p >= len(data["blockEdgeCount"]):
            sys.stderr.write(
                "a position, %d, is greater than or "
                "equal to len(data['blockEdgeCount']) %d [%d-%d]\n"
                % (p, len(data["blockEdgeCount"]), mb.refStart, mb.refEnd)
            )
        data["blockEdgeCount"][p] += 1.0
        if data["blockEdgeCount"][p] > data["blockEdgeMax"]:
            data["blockEdgeMax"] = data["blockEdgeCount"][p]
Esempio n. 3
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def objListUtility_addContigPathEdgeErrors(data, mb, featLen, numBins):
    """ Utility function for the MafBlock instance version of 
   libMafGffPlot.objListToBinnedWiggle()
   """
    from libMafGffPlot import objListUtility_indexToPos
    import math

    posSt = objListUtility_indexToPos(mb.refStart, featLen, numBins)
    posEnd = objListUtility_indexToPos(mb.refEnd, featLen, numBins)
    # five prime
    if mb.hplStart == 0:
        # edge
        data["mafCpEdgeCount"][posSt] += 1.0
        if data["mafCpEdgeCount"][posSt] > data["mafCpEdgeMax"]:
            data["mafCpEdgeMax"] = data["mafCpEdgeCount"][posSt]
    elif mb.hplStart == 2:
        # error
        data["mafCpErrorCount"][posSt] += 1.0
        if data["mafCpErrorCount"][posSt] > data["mafCpErrorMax"]:
            data["mafCpErrorMax"] = data["mafCpErrorCount"][posSt]
    elif mb.hplStart == 3:
        # scaffold gap
        data["mafCpScafGapCount"][posSt] += 1.0
        if data["mafCpScafGapCount"][posSt] > data["mafCpScafGapMax"]:
            data["mafCpScafGapMax"] = data["mafCpScafGapCount"][posSt]
    # three prime
    if mb.hplEnd == 0:
        # edge
        data["mafCpEdgeCount"][posEnd] += 1.0
        if data["mafCpEdgeCount"][posEnd] > data["mafCpEdgeMax"]:
            data["mafCpEdgeMax"] = data["mafCpEdgeCount"][posEnd]
    elif mb.hplEnd == 2:
        # error
        data["mafCpErrorCount"][posEnd] += 1.0
        if data["mafCpErrorCount"][posEnd] > data["mafCpErrorMax"]:
            data["mafCpErrorMax"] = data["mafCpErrorCount"][posEnd]
    elif mb.hplEnd == 3:
        # scaffold gap
        data["mafCpScafGapCount"][posEnd] += 1.0
        if data["mafCpScafGapCount"][posEnd] > data["mafCpScafGapMax"]:
            data["mafCpScafGapMax"] = data["mafCpScafGapCount"][posEnd]
Esempio n. 4
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def objListUtility_addContigPathEdgeErrors(data, mb, featLen, numBins):
    """ Utility function for the MafBlock instance version of 
   libMafGffPlot.objListToBinnedWiggle()
   """
    from libMafGffPlot import objListUtility_indexToPos
    import math
    posSt = objListUtility_indexToPos(mb.refStart, featLen, numBins)
    posEnd = objListUtility_indexToPos(mb.refEnd, featLen, numBins)
    # five prime
    if mb.hplStart == 0:
        # edge
        data['mafCpEdgeCount'][posSt] += 1.0
        if data['mafCpEdgeCount'][posSt] > data['mafCpEdgeMax']:
            data['mafCpEdgeMax'] = data['mafCpEdgeCount'][posSt]
    elif mb.hplStart == 2:
        # error
        data['mafCpErrorCount'][posSt] += 1.0
        if data['mafCpErrorCount'][posSt] > data['mafCpErrorMax']:
            data['mafCpErrorMax'] = data['mafCpErrorCount'][posSt]
    elif mb.hplStart == 3:
        # scaffold gap
        data['mafCpScafGapCount'][posSt] += 1.0
        if data['mafCpScafGapCount'][posSt] > data['mafCpScafGapMax']:
            data['mafCpScafGapMax'] = data['mafCpScafGapCount'][posSt]
    # three prime
    if mb.hplEnd == 0:
        # edge
        data['mafCpEdgeCount'][posEnd] += 1.0
        if data['mafCpEdgeCount'][posEnd] > data['mafCpEdgeMax']:
            data['mafCpEdgeMax'] = data['mafCpEdgeCount'][posEnd]
    elif mb.hplEnd == 2:
        # error
        data['mafCpErrorCount'][posEnd] += 1.0
        if data['mafCpErrorCount'][posEnd] > data['mafCpErrorMax']:
            data['mafCpErrorMax'] = data['mafCpErrorCount'][posEnd]
    elif mb.hplEnd == 3:
        # scaffold gap
        data['mafCpScafGapCount'][posEnd] += 1.0
        if data['mafCpScafGapCount'][posEnd] > data['mafCpScafGapMax']:
            data['mafCpScafGapMax'] = data['mafCpScafGapCount'][posEnd]