def test_filter_reads(self):
ion_chunk = "NGS/_reaa.fastq"
blast_chunk = "NGS/_reaa.csv"
folder = "NGS"
NGS.filter_reads(ion_chunk, blast_chunk, folder)
# it should generate many gene_ files
result = glob.glob("NGS/gene*")
self.assertEqual(len(result), 21)
for i in result:
os.remove(i)
def test_filter_reads(self):
folder = "NGS"
for i in glob.glob(os.path.join("NGS", "gene*")):
os.remove(i)
ion_chunk = os.path.join("NGS", "reaa.fastq")
blast_chunk = os.path.join("NGS", "reaa.csv")
NGS.filter_reads(ion_chunk, blast_chunk, folder)
cmd = "cat " + os.path.join("NGS", "gene*")
cmd += " | grep -c '^@'"
p = subprocess.check_output(cmd, shell=True)
for i in glob.glob(os.path.join("NGS", "gene*")):
os.remove(i)
self.assertEqual(int(p.strip()), 23)
