def test_interpertBlast(self):
tempBlast = Blast("", "")
tempBlast.makeDatabase("test_data/reference.fasta")
tempBlast.aliasTool("test_data/reference.fasta", "test_data")
tempBlast.query = "test_data/contigs_1.fasta"
tempBlast.doBlast("test_data")
tempBlast.interpertBlast("test_data")
self.assertEqual(len(tempBlast.hitSet), 3)
def test_doBlast(self):
tempBlast = Blast("", "")
tempBlast.makeDatabase("test_data/reference.fasta")
tempBlast.aliasTool("test_data/reference.fasta", "test_data")
tempBlast.query = "test_data/contigs_1.fasta"
tempBlast.doBlast("test_data")
try:
outputFile = open("test_data/blastResult.csv")
testResult = True
for line in outputFile:
if "gi|49175990|ref|NC_000913.2|" not in line:
testResult = False
self.assertTrue(testResult)
except IOError as error:
self.fail(error)
def test_makeDatabase(self):
tempBlast = Blast("", "")
tempBlast.makeDatabase("test_data/reference.fasta")
workline = "blastdbcmd -db test_data/reference.fasta -info"
p = subprocess.Popen(workline, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
try:
stdout, stderr = p.communicate()
testResult = True
if p.returncode == 0:
if "1 sequences; 10,000 total bases" not in stdout:
testResult = False
self.assertTrue(testResult)
else:
raise EnvironmentError(stderr)
except EnvironmentError as error:
self.fail(error)
"/MapperUnique.gff"))
methodList.append(PrimerDesign.PrimerDesign.runMethodSubstract([methodList[1], methodList[2]], Main.Main.workDir +
"/DenovoUnique.gff"))
genome = PrimerDesign.PrimerDesign.readRefGenome(Main.Main.genomeAdd + Main.Main.refGenomeList[0])
blastList = list()
for PipMethod in methodList:
fastaFile = PipMethod.rstrip()[:-3]+"fa"
PrimerDesign.PrimerDesign.saveFasta(fastaFile, PrimerDesign.PrimerDesign.readGFF(PipMethod, genome))
blastList.append(fastaFile)
otherGenomes = copy.copy(Main.Main.refGenomeList)
del otherGenomes[0]
blastThread = list()
allAlias = ""
for genome in otherGenomes:
Blast.makeDatabase(str(genome), Main.Main.workDir)
allAlias += Main.Main.workDir + "/" + genome + " "
allAlias = allAlias.rstrip()
Blast.aliasTool(allAlias, Main.Main.workDir)
for blastItem in blastList:
blastResult = Blast(blastItem, otherGenomes)
blastResult.start()
blastThread.append(blastResult)
for blastItem in blastThread:
blastItem.join()
genome = PrimerDesign.PrimerDesign.readRefGenome(Main.Main.genomeAdd + Main.Main.refGenomeList[0])
for k, blastItem in enumerate(blastList):
item = blastItem.rstrip()[:-2]
thread = threading.Thread(PrimerDesign.PrimerDesign.generatePrimer3Input(
