def testRunBlastX(self):
"""
test running blastx
"""
## run the blast
self.blast = Blast(self.queryFile)
outFile = "adh-0-2.xml"
targetDB = os.path.join(self.BLASTDB, "uniprot_sprot")
start, stop = 0, 2
self.blast.run_blast(targetDB,
evalue=0.1,
start=start,
stop=stop,
cmd='blastx')
## read the blast
parser = ParseBlast(outFile)
parser.run()
## clean up
for fn in [
"adh-0-2_parsed.csv", "adh-0-2_parsed.log", "adh-0-2.fasta",
"adh-0-2.xml"
]:
self.assertTrue(os.path.exists(fn))
os.remove(fn)
def testGetQueryFile(self):
"""
test the function breaks the fasta file in to chunks
"""
self.blast = Blast(self.queryFile)
## index 0 to 2 should return 2 results [0,1]
start, stop = 0, 2
newQueryFile = self.blast.get_query_file(".", start, stop)
queryFileName = os.path.split(self.queryFile)[-1]
queryFilePath = os.path.join(
".",
re.sub("\.\w+", "", queryFileName, flags=re.IGNORECASE) +
"-%s-%s.fasta" % (start, stop))
self.assertTrue(os.path.exists(queryFilePath))
handleIn = open(newQueryFile, "r")
total = 0
for record in SeqIO.parse(handleIn, "fasta"):
total += 1
self.assertEqual(total, 2)
handleIn.close()
os.remove(queryFilePath)
def testRunBlastX(self):
"""
test running blastx
"""
## run the blast
self.blast = Blast(self.queryFile)
outFile = "adh-0-2.xml"
targetDB = os.path.join(self.BLASTDB, "uniprot_sprot")
start, stop = 0, 2
self.blast.run_blast(targetDB, evalue=0.1, start=start, stop=stop, cmd="blastx")
## read the blast
parser = ParseBlast(outFile)
parser.run()
## clean up
for fn in ["adh-0-2_parsed.csv", "adh-0-2_parsed.log", "adh-0-2.fasta", "adh-0-2.xml"]:
self.assertTrue(os.path.exists(fn))
os.remove(fn)
def testGetQueryFile(self):
"""
test the function breaks the fasta file in to chunks
"""
self.blast = Blast(self.queryFile)
## index 0 to 2 should return 2 results [0,1]
start, stop = 0, 2
newQueryFile = self.blast.get_query_file(".", start, stop)
queryFileName = os.path.split(self.queryFile)[-1]
queryFilePath = os.path.join(
".", re.sub("\.\w+", "", queryFileName, flags=re.IGNORECASE) + "-%s-%s.fasta" % (start, stop)
)
self.assertTrue(os.path.exists(queryFilePath))
handleIn = open(newQueryFile, "rU")
total = 0
for record in SeqIO.parse(handleIn, "fasta"):
total += 1
self.assertEqual(total, 2)
handleIn.close()
os.remove(queryFilePath)
class BlastTest(unittest.TestCase):
"""
Run a number of tests using taxa id 7227
"""
def setUp(self):
"""
connect to the database
"""
self.queryFile = os.path.join(os.path.dirname(__file__), "adh.fasta")
config = Configure()
self.BLASTDB = config.log["data"]
def testGetQueryFile(self):
"""
test the function breaks the fasta file in to chunks
"""
self.blast = Blast(self.queryFile)
## index 0 to 2 should return 2 results [0,1]
start, stop = 0, 2
newQueryFile = self.blast.get_query_file(".", start, stop)
queryFileName = os.path.split(self.queryFile)[-1]
queryFilePath = os.path.join(
".", re.sub("\.\w+", "", queryFileName, flags=re.IGNORECASE) + "-%s-%s.fasta" % (start, stop)
)
self.assertTrue(os.path.exists(queryFilePath))
handleIn = open(newQueryFile, "rU")
total = 0
for record in SeqIO.parse(handleIn, "fasta"):
total += 1
self.assertEqual(total, 2)
handleIn.close()
os.remove(queryFilePath)
def testRunBlastX(self):
"""
test running blastx
"""
## run the blast
self.blast = Blast(self.queryFile)
outFile = "adh-0-2.xml"
targetDB = os.path.join(self.BLASTDB, "uniprot_sprot")
start, stop = 0, 2
self.blast.run_blast(targetDB, evalue=0.1, start=start, stop=stop, cmd="blastx")
## read the blast
parser = ParseBlast(outFile)
parser.run()
## clean up
for fn in ["adh-0-2_parsed.csv", "adh-0-2_parsed.log", "adh-0-2.fasta", "adh-0-2.xml"]:
self.assertTrue(os.path.exists(fn))
os.remove(fn)
def testParallelBlast(self):
"""
test that we can create shell scripts to be run in a parallel env
"""
parBlast = ParallelBlast(self.queryFile, "swissprot")
parBlast.evalue = 0.05
chunks = 3
parBlast.create_scripts(chunks, "*****@*****.**")
# parBlast.submit()
shutil.rmtree(os.path.join(".", "cluster"))
class BlastTest(unittest.TestCase):
"""
Run a number of tests using taxa id 7227
"""
def setUp(self):
"""
connect to the database
"""
self.queryFile = os.path.join(os.path.dirname(__file__), "adh.fasta")
config = Configure()
self.BLASTDB = config.log['data']
def testGetQueryFile(self):
"""
test the function breaks the fasta file in to chunks
"""
self.blast = Blast(self.queryFile)
## index 0 to 2 should return 2 results [0,1]
start, stop = 0, 2
newQueryFile = self.blast.get_query_file(".", start, stop)
queryFileName = os.path.split(self.queryFile)[-1]
queryFilePath = os.path.join(
".",
re.sub("\.\w+", "", queryFileName, flags=re.IGNORECASE) +
"-%s-%s.fasta" % (start, stop))
self.assertTrue(os.path.exists(queryFilePath))
handleIn = open(newQueryFile, "r")
total = 0
for record in SeqIO.parse(handleIn, "fasta"):
total += 1
self.assertEqual(total, 2)
handleIn.close()
os.remove(queryFilePath)
def testRunBlastX(self):
"""
test running blastx
"""
## run the blast
self.blast = Blast(self.queryFile)
outFile = "adh-0-2.xml"
targetDB = os.path.join(self.BLASTDB, "uniprot_sprot")
start, stop = 0, 2
self.blast.run_blast(targetDB,
evalue=0.1,
start=start,
stop=stop,
cmd='blastx')
## read the blast
parser = ParseBlast(outFile)
parser.run()
## clean up
for fn in [
"adh-0-2_parsed.csv", "adh-0-2_parsed.log", "adh-0-2.fasta",
"adh-0-2.xml"
]:
self.assertTrue(os.path.exists(fn))
os.remove(fn)
def testParallelBlast(self):
"""
test that we can create shell scripts to be run in a parallel env
"""
parBlast = ParallelBlast(self.queryFile, 'swissprot')
parBlast.evalue = 0.05
chunks = 3
parBlast.create_scripts(chunks, "*****@*****.**")
#parBlast.submit()
shutil.rmtree(os.path.join(".", "cluster"))