Save each object using cPickle."""
import csv
import math
import cPickle
from sequence import Sequence
from geneBank import GeneBank
fileList = ["wt1.csv", "wt2.csv", "rny1.csv", "rny2.csv"]
for fileName in fileList:
geneFile = open('Spy49_allGenes.csv', 'rU')
genes = csv.reader(geneFile)
with open(fileName, 'rU') as readsFile:
reads = csv.reader(readsFile, delimiter='\t')
readsList = []
for row in reads:
readsList.append(float(row[2]))
geneBank = GeneBank()
for row in genes:
name = row[0]
start = int(row[1])
end = int(row[2])
orientation = row[3]
seq = Sequence(readsList, (start, end), name, orientation)
geneBank.add(seq)
geneBankName = "geneBank_" + fileName[0:-4] + ".txt"
geneBank.save(geneBankName)
geneFile.close()
"""Find all operon after-gaps that occur in the four operonBanks. """
geneBankFiles = ["geneBank_wt1.txt", "geneBank_wt2.txt", \
"geneBank_rny1.txt", "geneBank_rny2.txt"]
readsFiles = ["wt1.csv", "wt2.csv", "rny1.csv", "rny2.csv"]
operonBankFiles = [OperonBank("operonBank_wt1.txt"), \
OperonBank("operonBank_wt2.txt"), \
OperonBank("operonBank_rny1.txt"), \
OperonBank("operonBank_rny2.txt")]
gapList = []
n = 0
for i in xrange(4):
operonBank = operonBankFiles[i]
geneBank = GeneBank(geneBankFiles[i])
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])
