def operonFinder(geneBank, readsList):
"""Group genes into operons."""
operon1 = Operon("operon_1")
gene1 = geneBank[0]
operon1.add(gene1)
operonBank = OperonBank()
operonBank.add(operon1)
j = 0
for i in xrange(1, len(geneBank)):
currentOperon = operonBank[-1]
currentGene = geneBank[i]
previousGene = geneBank[i-1]
if operonJudge(previousGene, currentGene, readsList) == False:
currentOperon.add(currentGene)
else:
j += 1
name = "operon_" + str(j + 1)
operon = Operon(name)
operon.add(currentGene)
operonBank.add(operon)
for operon in operonBank:
operon.setOrientation()
operon.setLeftBound(operon[0].getStart())
operon.setRightBound(operon[-1].getEnd())
operon.setReads(readsList)
return operonBank
readsList = []
for row in reads:
readsList.append(float(row[2]))
n = 0
operon = Operon("operon_" + str(n + 1))
for gene in geneBank:
afterGap = gapList[n]
if geneBank.getIndex(gene.getName()) < afterGap:
operon.add(gene)
elif geneBank.getIndex(gene.getName()) == afterGap:
operon.add(gene)
print gene.getName()
n += 1
operonBankRD.add(operon)
operon.setLeftBound(operon[0].getStart())
operon.setRightBound(operon[-1].getEnd())
operon.setOrientation()
operon.setReads(readsList)
print operon.getName()
print str(operon)
operon = Operon("operon_" + str(n + 1))
j = 0
while j < len(operonBankRD) -1:
operon1 = operonBankRD[j]
operon2 = operonBankRD[j+1]
boundFinder(operon1, operon2, readsList)
print operon1.getName(), (operon1.getLeftBound(), operon1.getRightBound()), \
round(operon1.getAverageRead(), 2)
