def setUp(self): self.tmp_dir = os.path.join(tempfile.gettempdir(), 'test_macsyfinder_search_genes') if os.path.exists(self.tmp_dir): shutil.rmtree(self.tmp_dir) os.mkdir(self.tmp_dir) args = argparse.Namespace() args.sequence_db = self.find_data("base", "test_base.fa") args.db_type = 'gembase' args.models_dir = self.find_data('models') args.log_level = 30 args.out_dir = os.path.join(self.tmp_dir, 'job_1') args.res_search_dir = args.out_dir os.mkdir(args.out_dir) self.cfg = Config(MacsyDefaults(), args) self.model_name = 'foo' self.model_location = ModelLocation( path=os.path.join(args.models_dir, self.model_name)) idx = Indexes(self.cfg) idx._build_my_indexes() self.profile_factory = ProfileFactory(self.cfg)
def test_fill_ordered_replicon_min_max(self): self.tearDown() self.cfg = Config(hmmer_exe="hmmsearch", sequence_db=os.path.join(self._data_dir, "base", "ordered_replicon_base"), db_type="ordered_replicon", e_value_res=1, i_evalue_sel=0.5, def_dir=os.path.join(self._data_dir, 'DEF'), res_search_dir='/tmp', res_search_suffix=".search_hmm.out", profile_dir=os.path.join(self._data_dir, 'profiles'), profile_suffix=".hmm", res_extract_suffix="", log_level=30, log_file='/dev/null') shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options['sequence_db'] = os.path.join( self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) idx = Indexes(self.cfg) idx._build_my_indexes() RepliconDB.__init__ = self.fake_init db = RepliconDB(self.cfg) db._fill_ordered_min_max(self.cfg.replicon_topology) self.assertEqual(len(db._DB), 1) rep = db[RepliconDB.ordered_replicon_name] self.assertEqual(rep.topology, self.cfg.replicon_topology) self.assertEqual(rep.min, 1) self.assertEqual(rep.max, 52)
def test_fill_ordered_replicon_min_max(self): self.tearDown() self.cfg = Config( hmmer_exe = "hmmsearch", sequence_db = os.path.join(self._data_dir, "base", "ordered_replicon_base"), db_type = "ordered_replicon", e_value_res = 1, i_evalue_sel = 0.5, def_dir = os.path.join(self._data_dir, 'DEF'), res_search_dir = tempfile.gettempdir(), res_search_suffix = ".search_hmm.out", profile_dir = os.path.join(self._data_dir, 'profiles'), profile_suffix = ".hmm", res_extract_suffix = "", log_level = 30, log_file = 'NUL' if platform.system() == 'Windows' else '/dev/null' ) shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options['sequence_db'] = os.path.join(self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) idx = Indexes(self.cfg) idx._build_my_indexes() RepliconDB.__init__ = self.fake_init db = RepliconDB(self.cfg) db._fill_ordered_min_max(self.cfg.replicon_topology) self.assertEqual(len(db._DB), 1) rep = db[RepliconDB.ordered_replicon_name] self.assertEqual(rep.topology, self.cfg.replicon_topology) self.assertEqual(rep.min, 1) self.assertEqual(rep.max, 52)
def setUp(self): l = logging.getLogger() l.manager.loggerDict.clear() # add only one handler to the macsypy logger from macsypy.gene import _log macsy_log = _log.parent log_file = 'NUL' if platform.system() == 'Windows' else '/dev/null' log_handler = logging.FileHandler(log_file) macsy_log.addHandler(log_handler) self.cfg = Config(hmmer_exe="hmmsearch", sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"), db_type="gembase", e_value_res=1, i_evalue_sel=0.5, def_dir=os.path.join(self._data_dir, 'DEF'), res_search_dir=tempfile.gettempdir(), res_search_suffix=".search_hmm.out", profile_dir=os.path.join(self._data_dir, 'profiles'), profile_suffix=".hmm", res_extract_suffix="", log_level=30, log_file=log_file) shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options['sequence_db'] = os.path.join( self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) self.profile_registry = ProfilesRegistry(self.cfg) idx = Indexes(self.cfg) idx._build_my_indexes()
def setUp(self): args = argparse.Namespace() args.db_type = 'gembase' args.models_dir = self.find_data('models') args.res_search_dir = tempfile.gettempdir() args.log_level = 30 args.out_dir = os.path.join(args.res_search_dir, 'test_macsyfinder_Report') if os.path.exists(args.out_dir): shutil.rmtree(args.out_dir) os.mkdir(args.out_dir) seq_db = self.find_data("base", "test_base.fa") shutil.copy(seq_db, args.out_dir) args.sequence_db = os.path.join(args.out_dir, os.path.basename(seq_db)) self.cfg = Config(MacsyDefaults(), args) os.mkdir(os.path.join(self.cfg.out_dir(), self.cfg.hmmer_dir())) self.model_name = 'foo' self.model_location = ModelLocation( path=os.path.join(args.models_dir, self.model_name)) # we need to reset the ProfileFactory # because it's a like a singleton # so other tests are influenced by ProfileFactory and it's configuration # for instance search_genes get profile without hmmer_exe self.profile_factory = ProfileFactory(self.cfg) idx = Indexes(self.cfg) idx._build_my_indexes()
def setUp(self): l = logging.getLogger() l.manager.loggerDict.clear() # add only one handler to the macsypy logger from macsypy.gene import _log macsy_log = _log.parent log_file = "NUL" if platform.system() == "Windows" else "/dev/null" log_handler = logging.FileHandler(log_file) macsy_log.addHandler(log_handler) self.cfg = Config( hmmer_exe="hmmsearch", sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"), db_type="gembase", e_value_res=1, i_evalue_sel=0.5, def_dir=os.path.join(self._data_dir, "DEF"), res_search_dir=tempfile.gettempdir(), res_search_suffix=".search_hmm.out", profile_dir=os.path.join(self._data_dir, "profiles"), profile_suffix=".hmm", res_extract_suffix="", log_level=30, log_file=log_file, ) shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options["sequence_db"] = os.path.join(self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) self.profile_registry = ProfilesRegistry(self.cfg) idx = Indexes(self.cfg) idx._build_my_indexes()
def test_build_my_indexes(self): args = argparse.Namespace() args.db_type = 'gembase' args.out_dir = os.path.join(tempfile.gettempdir(), 'test_macsyfinder_indexes') if os.path.exists(args.out_dir): shutil.rmtree( os.path.join(tempfile.gettempdir(), 'test_macsyfinder_indexes')) os.makedirs(args.out_dir) seq_db = self.find_data("base", "test_base_with_errors.fa") shutil.copy(seq_db, args.out_dir) args.sequence_db = os.path.join(args.out_dir, os.path.basename(seq_db)) self.cfg = Config(MacsyDefaults(), args) idx = Indexes(self.cfg) with self.assertRaises(MacsypyError) as e: # the directory for index exist and is writable but # the sequence file is corrupted and cannot be read correctly with self.catch_log(): idx._build_my_indexes(args.out_dir) self.assertTrue( str(e.exception).startswith( "unable to index the sequence dataset:"))
def setUp(self): l = logging.getLogger() l.manager.loggerDict.clear() self.cfg = Config( hmmer_exe = "hmmsearch", sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"), db_type = "gembase", e_value_res = 1, i_evalue_sel = 0.5, def_dir = os.path.join(self._data_dir, 'DEF'), res_search_dir = tempfile.gettempdir(), res_search_suffix = ".search_hmm.out", profile_dir = os.path.join(self._data_dir, 'profiles'), profile_suffix = ".hmm", res_extract_suffix = "", log_level = 30, log_file = 'NUL' if platform.system() == 'Windows' else '/dev/null' ) shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options['sequence_db'] = os.path.join(self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) self.ESCO030p01_genes = [('000010', '886'), ('000020', '291'), ('000030', '656'), ('000040', '500'), ('000050', '407'), ('000060', '144'), ('000070', '183'), ('000080', '121'), ('000090', '199'), ('000100', '325'), ('000110', '425'), ('000120', '171'), ('000130', '277'), ('000140', '133'), ('000150', '108'), ('000160', '295'), ('000170', '273'), ('000180', '367'), ('000190', '573'), ('000200', '343'), ('000210', '295'), ('000220', '108'), ('000230', '117'), ('000240', '153'), ('000250', '479'), ('000260', '706'), ('000270', '998'), ('000280', '171'), ('000290', '108'), ('000300', '295'), ('000310', '165'), ('000320', '243'), ('000330', '295'), ('000340', '108'), ('000350', '1755'), ('000360', '248'), ('000370', '286'), ('000380', '186'), ('000390', '83'), ('000400', '153'), ('000410', '69'), ('000420', '295'), ('000430', '108'), ('000440', '145'), ('000450', '59'), ('000460', '124'), ('000470', '246'), ('000480', '325'), ('000490', '54'), ('000500', '95'), ('000510', '83'), ('000520', '56'), ('000530', '401'), ('000540', '320'), ('000550', '256'), ('000560', '73'), ('000570', '144'), ('000580', '258'), ('000590', '133'), ('000600', '140'), ('000610', '63'), ('000620', '138'), ('000630', '68'), ('000640', '169'), ('000650', '127'), ('000660', '295'), ('000670', '108'), ('000670', '108')] self.PSAE001c01_genes = [('006940', '803'), ('013980', '759'), ('017350', '600'), ('018920', '776'), ('026600', '273'), ('031420', '658'), ('043580', '416'), ('051090', '714'), ('055870', '449'), ('055880', '447'), ('055890', '588'), ('055900', '292'), ('055910', '262'), ('055920', '166'), ('055930', '288'), ('055940', '194'), ('055950', '567'), ('055960', '188'), ('055970', '247'), ('055980', '252'), ('055990', '455'), ('056000', '450'), ('056010', '260'), ('056020', '246'), ('056030', '70'), ('056040', '133'), ('056050', '284'), ('056060', '585'), ('056070', '435'), ('056080', '342'), ('056090', '252'), ('056100', '122'), ('056110', '213'), ('056120', '400'), ('056130', '134'), ('056140', '138'), ('056150', '397'), ('056160', '298'), ('056170', '186'), ('056180', '445'), ('056190', '414'), ('056200', '132'), ('056210', '674'), ('056220', '319'), ('056230', '394'), ('056240', '207'), ('056250', '401'), ('056260', '611'), ('056270', '257'), ('056280', '169'), ('056290', '454'), ('056300', '141'), ('056310', '458'), ('056320', '286'), ('056330', '514'), ('056340', '178'), ('056350', '156'), ('056360', '85'), ('056370', '289'), ('056380', '126'), ('056390', '290'), ('056400', '262'), ('056410', '214'), ('056420', '630'), ('056430', '127'), ('056440', '455'), ('056440', '455')] idx = Indexes(self.cfg) idx._build_my_indexes()
def test_fill_ordered_replicon_min_max(self): seq_ori = self.find_data("base", "ordered_replicon_base.fasta") shutil.copy(seq_ori, self.args.out_dir) self.args.sequence_db = os.path.join(self.args.out_dir, os.path.basename(seq_ori)) cfg = Config(MacsyDefaults(), self.args) idx = Indexes(cfg) idx._build_my_indexes() RepliconDB.__init__ = self.fake_init db = RepliconDB(cfg) db._fill_ordered_min_max(cfg.replicon_topology()) self.assertEqual(len(db._DB), 1) rep = db[RepliconDB.ordered_replicon_name] self.assertEqual(rep.topology, cfg.replicon_topology()) self.assertEqual(rep.min, 1) self.assertEqual(rep.max, 52)
def setUp(self): self.cfg = Config( hmmer_exe = "hmmsearch", sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"), db_type = "gembase", e_value_res = 1, i_evalue_sel = 0.5, def_dir = os.path.join(self._data_dir, 'DEF'), res_search_dir = '/tmp', res_search_suffix = ".search_hmm.out", profile_dir = os.path.join(self._data_dir, 'profiles'), profile_suffix = ".hmm", res_extract_suffix = "", log_level = 30, log_file = '/dev/null' ) shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options['sequence_db'] = os.path.join(self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) self.profile_registry = ProfilesRegistry(self.cfg) idx = Indexes(self.cfg) idx._build_my_indexes()
def setUp(self): self.cfg = Config(hmmer_exe="hmmsearch", sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"), db_type="gembase", e_value_res=1, i_evalue_sel=0.5, def_dir=os.path.join(self._data_dir, 'DEF'), res_search_dir='/tmp', res_search_suffix=".search_hmm.out", profile_dir=os.path.join(self._data_dir, 'profiles'), profile_suffix=".hmm", res_extract_suffix="", log_level=30, log_file='/dev/null') shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options['sequence_db'] = os.path.join( self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) self.profile_registry = ProfilesRegistry(self.cfg) idx = Indexes(self.cfg) idx._build_my_indexes()
def setUp(self): l = logging.getLogger() l.manager.loggerDict.clear() self.cfg = Config( hmmer_exe = "hmmsearch", sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"), db_type = "gembase", e_value_res = 1, i_evalue_sel = 0.5, def_dir = os.path.join(self._data_dir, 'DEF'), res_search_dir = tempfile.gettempdir(), res_search_suffix = ".search_hmm.out", profile_dir = os.path.join(self._data_dir, 'profiles'), profile_suffix = ".hmm", res_extract_suffix = "", log_level = 30, log_file = 'NUL' if platform.system() == 'Windows' else '/dev/null' ) shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options['sequence_db'] = os.path.join(self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) self.profile_registry = ProfilesRegistry(self.cfg) idx = Indexes(self.cfg) idx._build_my_indexes()
def test_build_my_indexes(self): args = argparse.Namespace() args.db_type = 'gembase' args.e_value_res = 1 args.i_evalue_sel = 0.5 args.models_dir = self.find_data('models') args.res_search_suffix = '' args.log_level = 30 args.out_dir = os.path.join(tempfile.gettempdir(), 'test_macsyfinder_indexes') if os.path.exists(args.out_dir): shutil.rmtree(os.path.join(tempfile.gettempdir(), 'test_macsyfinder_indexes')) os.makedirs(args.out_dir) seq_db = self.find_data("base", "test_base_with_errors.fa") shutil.copy(seq_db, args.out_dir) args.sequence_db = os.path.join(args.out_dir, os.path.basename(seq_db)) cfg = Config(MacsyDefaults(), args) idx = Indexes(cfg) with self.assertRaises(MacsypyError) as e: with self.catch_log(): idx._build_my_indexes() self.assertTrue(str(e.exception).startswith("unable to index the sequence dataset:"))
def setUp(self): self.cfg = Config(hmmer_exe="hmmsearch", sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"), db_type="gembase", e_value_res=1, i_evalue_sel=0.5, def_dir=os.path.join(self._data_dir, 'DEF'), res_search_dir='/tmp', res_search_suffix=".search_hmm.out", profile_dir=os.path.join(self._data_dir, 'profiles'), profile_suffix=".hmm", res_extract_suffix="", log_level=30, log_file='/dev/null') shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options['sequence_db'] = os.path.join( self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) self.ESCO030p01_genes = [('000010', '886'), ('000020', '291'), ('000030', '656'), ('000040', '500'), ('000050', '407'), ('000060', '144'), ('000070', '183'), ('000080', '121'), ('000090', '199'), ('000100', '325'), ('000110', '425'), ('000120', '171'), ('000130', '277'), ('000140', '133'), ('000150', '108'), ('000160', '295'), ('000170', '273'), ('000180', '367'), ('000190', '573'), ('000200', '343'), ('000210', '295'), ('000220', '108'), ('000230', '117'), ('000240', '153'), ('000250', '479'), ('000260', '706'), ('000270', '998'), ('000280', '171'), ('000290', '108'), ('000300', '295'), ('000310', '165'), ('000320', '243'), ('000330', '295'), ('000340', '108'), ('000350', '1755'), ('000360', '248'), ('000370', '286'), ('000380', '186'), ('000390', '83'), ('000400', '153'), ('000410', '69'), ('000420', '295'), ('000430', '108'), ('000440', '145'), ('000450', '59'), ('000460', '124'), ('000470', '246'), ('000480', '325'), ('000490', '54'), ('000500', '95'), ('000510', '83'), ('000520', '56'), ('000530', '401'), ('000540', '320'), ('000550', '256'), ('000560', '73'), ('000570', '144'), ('000580', '258'), ('000590', '133'), ('000600', '140'), ('000610', '63'), ('000620', '138'), ('000630', '68'), ('000640', '169'), ('000650', '127'), ('000660', '295'), ('000670', '108'), ('000670', '108')] self.PSAE001c01_genes = [('006940', '803'), ('013980', '759'), ('017350', '600'), ('018920', '776'), ('026600', '273'), ('031420', '658'), ('043580', '416'), ('051090', '714'), ('055870', '449'), ('055880', '447'), ('055890', '588'), ('055900', '292'), ('055910', '262'), ('055920', '166'), ('055930', '288'), ('055940', '194'), ('055950', '567'), ('055960', '188'), ('055970', '247'), ('055980', '252'), ('055990', '455'), ('056000', '450'), ('056010', '260'), ('056020', '246'), ('056030', '70'), ('056040', '133'), ('056050', '284'), ('056060', '585'), ('056070', '435'), ('056080', '342'), ('056090', '252'), ('056100', '122'), ('056110', '213'), ('056120', '400'), ('056130', '134'), ('056140', '138'), ('056150', '397'), ('056160', '298'), ('056170', '186'), ('056180', '445'), ('056190', '414'), ('056200', '132'), ('056210', '674'), ('056220', '319'), ('056230', '394'), ('056240', '207'), ('056250', '401'), ('056260', '611'), ('056270', '257'), ('056280', '169'), ('056290', '454'), ('056300', '141'), ('056310', '458'), ('056320', '286'), ('056330', '514'), ('056340', '178'), ('056350', '156'), ('056360', '85'), ('056370', '289'), ('056380', '126'), ('056390', '290'), ('056400', '262'), ('056410', '214'), ('056420', '630'), ('056430', '127'), ('056440', '455'), ('056440', '455')] idx = Indexes(self.cfg) idx._build_my_indexes()
def setUp(self): l = logging.getLogger() l.manager.loggerDict.clear() #add only one handler to the macsypy logger from macsypy.database import _log macsy_log = _log.parent log_file = 'NUL' if platform.system() == 'Windows' else '/dev/null' log_handler = logging.FileHandler(log_file) macsy_log.addHandler(log_handler) self.cfg = Config( hmmer_exe = "hmmsearch", sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"), db_type = "gembase", e_value_res = 1, i_evalue_sel = 0.5, def_dir = os.path.join(self._data_dir, 'DEF'), res_search_dir = tempfile.gettempdir(), res_search_suffix = ".search_hmm.out", profile_dir = os.path.join(self._data_dir, 'profiles'), profile_suffix = ".hmm", res_extract_suffix = "", log_level = 30, log_file = log_file ) shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options['sequence_db'] = os.path.join(self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) self.ESCO030p01_genes = [('000010', '886'), ('000020', '291'), ('000030', '656'), ('000040', '500'), ('000050', '407'), ('000060', '144'), ('000070', '183'), ('000080', '121'), ('000090', '199'), ('000100', '325'), ('000110', '425'), ('000120', '171'), ('000130', '277'), ('000140', '133'), ('000150', '108'), ('000160', '295'), ('000170', '273'), ('000180', '367'), ('000190', '573'), ('000200', '343'), ('000210', '295'), ('000220', '108'), ('000230', '117'), ('000240', '153'), ('000250', '479'), ('000260', '706'), ('000270', '998'), ('000280', '171'), ('000290', '108'), ('000300', '295'), ('000310', '165'), ('000320', '243'), ('000330', '295'), ('000340', '108'), ('000350', '1755'), ('000360', '248'), ('000370', '286'), ('000380', '186'), ('000390', '83'), ('000400', '153'), ('000410', '69'), ('000420', '295'), ('000430', '108'), ('000440', '145'), ('000450', '59'), ('000460', '124'), ('000470', '246'), ('000480', '325'), ('000490', '54'), ('000500', '95'), ('000510', '83'), ('000520', '56'), ('000530', '401'), ('000540', '320'), ('000550', '256'), ('000560', '73'), ('000570', '144'), ('000580', '258'), ('000590', '133'), ('000600', '140'), ('000610', '63'), ('000620', '138'), ('000630', '68'), ('000640', '169'), ('000650', '127'), ('000660', '295'), ('000670', '108'), ('000670', '108')] self.PSAE001c01_genes = [('006940', '803'), ('013980', '759'), ('017350', '600'), ('018920', '776'), ('026600', '273'), ('031420', '658'), ('043580', '416'), ('051090', '714'), ('055870', '449'), ('055880', '447'), ('055890', '588'), ('055900', '292'), ('055910', '262'), ('055920', '166'), ('055930', '288'), ('055940', '194'), ('055950', '567'), ('055960', '188'), ('055970', '247'), ('055980', '252'), ('055990', '455'), ('056000', '450'), ('056010', '260'), ('056020', '246'), ('056030', '70'), ('056040', '133'), ('056050', '284'), ('056060', '585'), ('056070', '435'), ('056080', '342'), ('056090', '252'), ('056100', '122'), ('056110', '213'), ('056120', '400'), ('056130', '134'), ('056140', '138'), ('056150', '397'), ('056160', '298'), ('056170', '186'), ('056180', '445'), ('056190', '414'), ('056200', '132'), ('056210', '674'), ('056220', '319'), ('056230', '394'), ('056240', '207'), ('056250', '401'), ('056260', '611'), ('056270', '257'), ('056280', '169'), ('056290', '454'), ('056300', '141'), ('056310', '458'), ('056320', '286'), ('056330', '514'), ('056340', '178'), ('056350', '156'), ('056360', '85'), ('056370', '289'), ('056380', '126'), ('056390', '290'), ('056400', '262'), ('056410', '214'), ('056420', '630'), ('056430', '127'), ('056440', '455'), ('056440', '455')] self.NCDB_genes = [('056134', '289'), ('056135', '126'), ('056136', '290'), ('056137', '262'), ('056138', '214'), ('056139', '630'), ('056140', '127'), ('056141', '803'), ('056141', '803')] idx = Indexes(self.cfg) idx._build_my_indexes()
def setUp(self): self.args = argparse.Namespace() self.args.db_type = 'gembase' self.args.models_dir = self.find_data('models') self.args.res_search_dir = tempfile.gettempdir() self.args.log_level = 30 self.args.out_dir = os.path.join(self.args.res_search_dir, 'test_macsyfinder_repliconDB') if os.path.exists(self.args.out_dir): shutil.rmtree(self.args.out_dir) os.mkdir(self.args.out_dir) seq_db = self.find_data("base", "test_base.fa") shutil.copy(seq_db, self.args.out_dir) self.args.sequence_db = os.path.join(self.args.out_dir, os.path.basename(seq_db)) self.cfg = Config(MacsyDefaults(), self.args) self.ESCO030p01_genes = [('000010', '886'), ('000020', '291'), ('000030', '656'), ('000040', '500'), ('000050', '407'), ('000060', '144'), ('000070', '183'), ('000080', '121'), ('000090', '199'), ('000100', '325'), ('000110', '425'), ('000120', '171'), ('000130', '277'), ('000140', '133'), ('000150', '108'), ('000160', '295'), ('000170', '273'), ('000180', '367'), ('000190', '573'), ('000200', '343'), ('000210', '295'), ('000220', '108'), ('000230', '117'), ('000240', '153'), ('000250', '479'), ('000260', '706'), ('000270', '998'), ('000280', '171'), ('000290', '108'), ('000300', '295'), ('000310', '165'), ('000320', '243'), ('000330', '295'), ('000340', '108'), ('000350', '1755'), ('000360', '248'), ('000370', '286'), ('000380', '186'), ('000390', '83'), ('000400', '153'), ('000410', '69'), ('000420', '295'), ('000430', '108'), ('000440', '145'), ('000450', '59'), ('000460', '124'), ('000470', '246'), ('000480', '325'), ('000490', '54'), ('000500', '95'), ('000510', '83'), ('000520', '56'), ('000530', '401'), ('000540', '320'), ('000550', '256'), ('000560', '73'), ('000570', '144'), ('000580', '258'), ('000590', '133'), ('000600', '140'), ('000610', '63'), ('000620', '138'), ('000630', '68'), ('000640', '169'), ('000650', '127'), ('000660', '295'), ('000670', '108'), ('000670', '108')] self.PSAE001c01_genes = [('006940', '803'), ('013980', '759'), ('017350', '600'), ('018920', '776'), ('026600', '273'), ('031420', '658'), ('043580', '416'), ('051090', '714'), ('055870', '449'), ('055880', '447'), ('055890', '588'), ('055900', '292'), ('055910', '262'), ('055920', '166'), ('055930', '288'), ('055940', '194'), ('055950', '567'), ('055960', '188'), ('055970', '247'), ('055980', '252'), ('055990', '455'), ('056000', '450'), ('056010', '260'), ('056020', '246'), ('056030', '70'), ('056040', '133'), ('056050', '284'), ('056060', '585'), ('056070', '435'), ('056080', '342'), ('056090', '252'), ('056100', '122'), ('056110', '213'), ('056120', '400'), ('056130', '134'), ('056140', '138'), ('056150', '397'), ('056160', '298'), ('056170', '186'), ('056180', '445'), ('056190', '414'), ('056200', '132'), ('056210', '674'), ('056220', '319'), ('056230', '394'), ('056240', '207'), ('056250', '401'), ('056260', '611'), ('056270', '257'), ('056280', '169'), ('056290', '454'), ('056300', '141'), ('056310', '458'), ('056320', '286'), ('056330', '514'), ('056340', '178'), ('056350', '156'), ('056360', '85'), ('056370', '289'), ('056380', '126'), ('056390', '290'), ('056400', '262'), ('056410', '214'), ('056420', '630'), ('056430', '127'), ('056440', '455'), ('056440', '455')] self.NCDB_genes = [('056134', '289'), ('056135', '126'), ('056136', '290'), ('056137', '262'), ('056138', '214'), ('056139', '630'), ('056140', '127'), ('056141', '803'), ('056141', '803')] idx = Indexes(self.cfg) idx._build_my_indexes()