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)