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
for operon in operonBank:
gene = operon[-1]
gap = geneBank.getIndex(gene.getName())
if gap not in gapList:
gapList.append(gap)
n += 1
print "The number of after-gaps is: ", n
gapList.sort()
"""Group genes into operons based on the gap information """
for i in xrange(len(geneBankFiles)):
geneBank = GeneBank(geneBankFiles[i])
operonBankRD = OperonBank()
with open(readsFiles[i], 'rU') as readsFile:
reads = csv.reader(readsFile, delimiter='\t')
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)
