def testDel(string, i, c):
fm = fmindex.createFM(string)
before = fm.bwt
fm.delBase(i)
afterString = string[:i] + c + string[i:]
afterfm = fmindex.FMindex(afterString)
if afterfm.bwt == fm.bwt:
output.extend(["PASS: "******" " + n.format(str(i))])
else:
output.extend(["FAIL: " + c + " " + n.format(str(i))])
return fm
def main():
string = sys.argv[1]
if '$' in string:
print "Don't include $ in genome"
sys.exit(0)
fm = fmindex.createFM(string)
if fm.getInverse() != string:
print "LF function does not correctly inverse BWT. Not equal", string, fm.getInverse()
sys.exit(0)
if len(sys.argv) == 4:
fm = testIns(string, int(sys.argv[3]), sys.argv[2])
else:
stressTest(string)
def stressTest(string):
numCorrect = 0
numTotal = 0
for i in range(0, len(string) - 1):
for c in "ACGT":
fm = fmindex.createFM(string)
afterString = string[:i] + string[: i + 1]
afterfm = fmindex.FMindex(afterString)
fm = testDel(string, i, c)
if afterfm.bwt == fm.bwt:
numCorrect += 1
numTotal += 1
print "\n".join(output)
print string
print numCorrect, "PASS;", numTotal - numCorrect, "FAIL;", "SCORE:", float(numCorrect) / float(numTotal) * 100
def stressTest(string):
numCorrect = 0
numTotal = 0
for i in range(0, len(string)):
for c in "ACGT":
fm = fmindex.createFM(string)
# print "Testing i =", i, ", c =,", c
# print "Before: T =", string +'$ ', "BWT =", fm.bwt
afterString = string[:i] + c + string[i:]
afterfm = fmindex.FMindex(afterString)
fm = testIns(string, i, c)
if afterfm.bwt == fm.bwt:
numCorrect+=1
numTotal+=1
print '\n'.join(output)
print string
print numCorrect,"PASS;",numTotal-numCorrect,"FAIL;","SCORE:",float(numCorrect)/float(numTotal)*100
def testIns(string, i, c):
fm = fmindex.createFM(string)
before = fm.bwt
fm.insBase(i, c)
afterString = string[:i] + c + string[i:]
afterfm = fmindex.FMindex(afterString)
if afterfm.bwt == fm.bwt:
output.extend(["PASS: "******" " + n.format(str(i))])
else:
output.extend(["FAIL: " + c + " " + n.format(str(i))])
'''print "Correct result:", afterfm.bwt
print "Actual results:", fm.bwt
print " Actual | Correct"
for j in range(len(afterfm.bwt)):
correctResults=' '.join([str(afterfm.sa[j]),str(afterfm.isa[j]), sorted(afterfm.bwt)[j], afterfm.bwt[j]])
if j >= len(fm.bwt):
actualResults = " |"
else:
actualResults=' '.join([str(fm.sa[j]),str(fm.isa[j]),sorted(fm.bwt)[j],fm.bwt[j], "|"])
print actualResults, correctResults
'''
return fm
def setTemplate(self, genome): self.fm = fmindex.createFM(genome) #also fm.count, fm.occ, fm.sa
def __init__(self, genome): self.fm = fmindex.createFM(genome)