def setUp(self): cfg = EpacTrainerConfig() cfg.debug=True testfile_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "testfiles") tax_fname = os.path.join(testfile_dir, "test.tax") phy_fname = os.path.join(testfile_dir, "test.phy") tax = Taxonomy(EpacConfig.REF_SEQ_PREFIX, tax_fname) seqs = SeqGroup(sequences=phy_fname, format = "phylip") self.inval = InputValidator(cfg, tax, seqs, False) self.expected_mis_ids = ["Missing1", "Missing2"] self.expected_dups = ["DupSeq(01)", "DupSeq02"] self.expected_merges = [self.inval.taxonomy.seq_rank_id(sid) for sid in self.expected_dups]
def setUp(self): cfg = EpacTrainerConfig() cfg.debug = True testfile_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "testfiles") tax_fname = os.path.join(testfile_dir, "test.tax") phy_fname = os.path.join(testfile_dir, "test.phy") tax = Taxonomy(EpacConfig.REF_SEQ_PREFIX, tax_fname) seqs = SeqGroup(sequences=phy_fname, format="phylip") self.inval = InputValidator(cfg, tax, seqs, False) self.expected_mis_ids = ["Missing1", "Missing2"] self.expected_dups = ["DupSeq(01)", "DupSeq02"] self.expected_merges = [ self.inval.taxonomy.seq_rank_id(sid) for sid in self.expected_dups ]
print "or call this script with -no-hmmer option to skip building HMMER profile." config.exit_user_error() def run_trainer(config): check_dep(config) builder = RefTreeBuilder(config) builder.invocation_epac = " ".join(sys.argv) builder.build_ref_tree() # ------- # MAIN # ------- if __name__ == "__main__": args = parse_args() check_args(args) config = EpacTrainerConfig(args) print "" config.print_version("SATIVA-trainer") start_time = time.time() run_trainer(config) config.clean_tempdir() config.log.info("Reference JSON was saved to: %s", os.path.abspath(config.refjson_fname)) config.log.info("Execution log was saved to: %s\n", os.path.abspath(config.log_fname)) elapsed_time = time.time() - start_time config.log.info("Training completed successfully, elapsed time: %.0f seconds\n", elapsed_time)
def run_trainer(config): check_dep(config) builder = RefTreeBuilder(config) builder.invocation_epac = " ".join(sys.argv) builder.build_ref_tree() # ------- # MAIN # ------- if __name__ == "__main__": args = parse_args() check_args(args) config = EpacTrainerConfig(args) print "" config.print_version("SATIVA-trainer") start_time = time.time() run_trainer(config) config.clean_tempdir() config.log.info("Reference JSON was saved to: %s", os.path.abspath(config.refjson_fname)) config.log.info("Execution log was saved to: %s\n", os.path.abspath(config.log_fname)) elapsed_time = time.time() - start_time
def test_trainer_config(self): args = self.get_trainer_namespace() cfg = EpacTrainerConfig(args) self.check_common_config(cfg)