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]
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]
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]
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]