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)