def add_operon(self, feature_list, strand):
'''
Appends a new operon object to the genome fragment.
Parameters
----------
feature_list: list[GenomeFeature object]
List of features belonging to the operon
strand: string
The strand, + or -, that the operon is located on.
Returns
-------
None
'''
self.operons.append(
Operon(genome_fragment_name=self.name,
genome_accession=self.genome_accession,
genome_features=self.all_features,
strand=strand))
for f in feature_list:
self.operons[-1].add_feature(f)
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
"""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)
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)