def test_prepare_data(self): ionfile = os.path.join(self.cwd, "NGS", "ion_file.fastq") NGS.prepare_data(ionfile, 8) expected_file1 = os.path.join("data", "modified", "wrk_ionfile.fasta") expected_file2 = os.path.join("data", "modified", "wrk_ionfile.fastq") self.assertTrue(os.path.isfile(expected_file1)) self.assertTrue(os.path.isfile(expected_file2)) os.remove(expected_file1) os.remove(expected_file2)
from pyphylogenomics import NGS import sys ionfile = sys.argv[1].strip() index_length = 0; NGS.prepare_data(ionfile, index_length);