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)