def test_do_blast(self):
f = os.path.join(self.cwd, "BLAST", "query.fas")
genome = os.path.join(self.cwd, "BLAST", "silkcds.fa")
BLAST.makeblastdb(genome)
command = (
"blastn -query "
+ f
+ " -db "
+ genome
+ " -task blastn "
+ "-evalue 0.0001 "
+ " -out "
+ f
+ "_out.csv"
+ " -num_threads 1 "
+ " -outfmt 10"
)
BLAST.do_blast(command)
output = open(os.path.join(self.cwd, "BLAST", "query.fas_out.csv"), "r")
for line in output:
self.assertTrue("BGIBMGA000001" in line)
break
for name in os.listdir(self.cwd + "/BLAST/"):
if name[:10] == "silkcds.fa" and len(name) > 10:
os.remove(self.cwd + "/BLAST/" + name)
os.remove(os.path.join(self.cwd, "BLAST", "query.fas_out.csv"))
def test_makeblastdb_false(self):
mask = False
BLAST.makeblastdb(self.genome, mask)
for name in os.listdir(self.cwd + "/BLAST/"):
if name[:10] == "silkcds.fa" and len(name) > 10:
os.remove(self.cwd + "/BLAST/" + name)
result = "true"
self.assertEqual(result, "true")
