def setUp(self): self.debug_folder = generic.setup_debug_folder(paths_test.DEBUG) self.input_seqfile = paths_test.MEME_TEST_SEQ self.input_memefile = paths_test.REF_MEME_TXT self.output = os.path.join(self.debug_folder, "output_meme") self.ref_output = paths_test.REF_MAST_DIAGRAMS self.success = False
def setUp(self): self.debug_folder = generic.setup_debug_folder(paths_test.DEBUG) self.prosite_input = paths_test.PROSITE_EXTRACT self.ioncom_input = paths_test.IONCOM_EXTRACT self.output = os.path.join(self.debug_folder, "output_1.pkl") self.prosite_ref = paths_test.REF_PROSITE_EXTRACT_PNAME_CID self.ioncom_ref = paths_test.REF_IONCOM_EXTRACT_PNAME_CID self.success = False
def setUp(self): self.debug_folder = generic.setup_debug_folder(paths_test.DEBUG) self.seq_path = paths_test.CONV_TEST_SEQ self.output = os.path.join(self.debug_folder, "output_1.pkl") self.binding_sites = paths_test.IONCOM_BINDING_SITES self.seed_seqs = paths_test.INPUT_CONV_SEED_SEQS self.ref_coverge_bind = paths_test.REF_CONV_WITH_BIND self.ref_converge_seed = paths_test.REF_CONV_WITH_SEED self.success = False
def setUp(self): self.debug_folder = generic.setup_debug_folder(paths_test.DEBUG) self.prosite_input = paths_test.PROSITE_EXTRACT self.ioncom_input = paths_test.IONCOM_EXTRACT self.output = os.path.join(self.debug_folder, "output_1.pkl") self.ref_meme_txt = paths_test.REF_MEME_TXT self.ref_prosite_meme = paths_test.REF_RUN_PROSITE_MEME self.ref_prosite_mast = paths_test.REF_RUN_PROSITE_MAST self.ref_ioncom_mast = paths_test.REF_RUN_IONCOM_MAST self.success = False
def setUp(self): self.debug_folder = generic.setup_debug_folder(paths_test.DEBUG) self.input_1 = paths_test.REF_PROSITE_EXTRACT_PNAME_CID self.input_2 = paths_test.REF_IONCOM_EXTRACT_PNAME_CID self.pdb_folder = paths_test.PDB_FOLDER self.output = os.path.join(self.debug_folder, "output_1.pkl") self.ref_output_1 = paths_test.REF_CREATE_SEQ_1 self.ref_output_2 = paths_test.REF_CREATE_SEQ_2 self.success = False
def setup_meme_suite_mast(): debug_folder = generic.setup_debug_folder(paths_test.DEBUG) mast_output_folder = os.path.join(debug_folder, "output_mast") input_seqfile = paths_test.MEME_TEST_SEQ input_memefile = paths_test.REF_MEME_TXT diagrams_output = paths_test.REF_MAST_DIAGRAMS meme_interface.run_mast(input_memefile, input_seqfile, mast_output_folder) mast_txt_path = os.path.join(mast_output_folder, "mast.txt") diagrams = bio_interface.parse_mast_file(mast_txt_path) with open(diagrams_output, 'wb') as file: pickle.dump(diagrams, file, -1)