def load_consensus_file_repeat_ids(self):
a = apply.Apply()
a.consensus = {}
consensus_file = os.path.join(data_dir, "consensus.fasta")
a.load_consensus_file(consensus_file)
self.assertRaises(AssertionError, a.load_consensus_file,
consensus_file)
def test_load_coordinates_file_no_feature_list(self):
coordinate_file = os.path.join(data_dir, "simple.coordinates")
features_list = None
a = apply.Apply()
a.coordinates = {}
a.load_coordinates_file(coordinate_file, features_list)
expect_coordinates = {
"ORF1": {
"seq1": {
"start": 0,
"end": 90
},
"seq3": {
"start": 10,
"end": 100
}
},
"ORF2": {
"seq2": {
"start": 0,
"end": 126
},
"seq3": {
"start": 10,
"end": 136
}
}
}
self.assertEqual(a.coordinates, expect_coordinates)
def run(options):
if options.verbose:
log_level = logging.DEBUG
msg = "Using debug logging"
else:
log_level = logging.INFO
msg = "Using info logging"
#log_file = f"apply.log"
#if os.path.exists(log_file):
# os.unlink(log_file)
logging.basicConfig(
#filename=log_file,
stream=sys.stdout,
level=log_level,
format="%(asctime)s\t%(levelname)s\t%(message)s",
datefmt="%d/%m/%Y %I:%M:%S",
)
logging.info(msg)
logging.info(
"Input parameters:\nDirectory: %s\nEdit file: %s\nFeatures: %s\nOutput prefix: %s\nConcatenate: %s"
%(options.directory,
options.edit_file,
options.features,
options.output_prefix,
options.concatinate)
)
g = apply.Apply()
g.run(options.directory, options.edit_file, options.output_prefix, options.features, options.concatinate)
def test_apply_loaded_edits_edits_empty(self):
a = apply.Apply()
editfile = os.path.join(data_dir, "all.edits")
a.load_input_files(data_dir, edit_filepath=editfile)
a.edits = EditFile()
a.apply_loaded_edits()
for name in a.consensus_sequence:
self.assertEqual(a.consensus_sequence[name].seq,
self.a.consensus_sequence[name].seq)
def test_run_with_no_features_concat(self):
a = apply.Apply()
editfile = os.path.join(data_dir, 'all.edits')
tmp_prefix = os.path.join(data_dir, 'tmp')
a.run(data_dir, editfile, tmp_prefix, concat=True)
tmp_na_file = os.path.join(data_dir, 'tmp.na.fasta')
expect_na_file = os.path.join(
data_dir, 'expect_updated_na_consensus_concat.fasta')
self.assertTrue(filecmp.cmp(tmp_na_file, expect_na_file,
shallow=False))
os.unlink(tmp_na_file)
tmp_aa_file = os.path.join(data_dir, 'tmp.aa.fasta')
expect_aa_file = os.path.join(
data_dir, 'expect_updated_aa_consensus_concat.fasta')
self.assertTrue(filecmp.cmp(tmp_aa_file, expect_aa_file,
shallow=False))
os.unlink(tmp_aa_file)
def test_load_coordinates_file_with_feature_list(self):
coordinate_file = os.path.join(data_dir, "simple.coordinates")
features_list = ["ORF1", "idontexistinasample"]
a = apply.Apply()
a.coordinates = {}
a.load_coordinates_file(coordinate_file, features_list)
expect_coordinates = {
"ORF1": {
"seq1": {
"start": 0,
"end": 90
},
"seq3": {
"start": 10,
"end": 100
}
},
"idontexistinasample": {}
}
self.assertEqual(a.coordinates, expect_coordinates)
def test_load_edits_in_range_with_feature_list(self):
a = apply.Apply()
edit_file = os.path.join(data_dir, "simple_edits")
features_list = ["ORF1", "idontexistinasample"]
a.coordinates = {
"ORF1": {
"seq1": {
"start": 0,
"end": 90
},
"seq3": {
"start": 10,
"end": 100
}
},
"idontexistinasample": {}
}
a.load_edits_in_range(edit_file, features_list)
expect_edit_file = os.path.join(data_dir, "simple_edits_expect")
expect_edits = EditFile(expect_edit_file)
self.assertEqual(a.edits, expect_edits)
def test_load_coordinates_file_with_join(self):
coordinate_file = os.path.join(data_dir, "simple2.coordinates")
features_list = ["ORF3", "idontexistinasample"]
a = apply.Apply()
a.coordinates = {}
a.load_coordinates_file(coordinate_file, features_list)
expect_coordinates = {
"ORF3": {
"seq6": {
"join": [{
"start": 0,
"end": 124
}, {
"start": 125,
"end": 128
}]
}
},
"idontexistinasample": {}
}
self.assertEqual(a.coordinates, expect_coordinates)
def setUp(self):
self.a = apply.Apply()
editfile = os.path.join(data_dir, 'all.edits')
self.a.load_input_files(data_dir, editfile)
def test_load_input_files_empty(self):
a = apply.Apply()
edit_file = os.path.join(data_dir, "all.edits")
empty_dir = os.path.join(data_dir, "empty")
self.assertRaises(AssertionError, a.load_input_files, empty_dir,
edit_file)
def load_consensus_file(self):
a = apply.Apply()
a.consensus = {}
consensus_file = os.path.join(data_dir, "consensus.fasta")
a.load_consensus_file(consensus_file)
self.assertEqual(len(a.consensus_sequence), 12)
def test_load_consensus_file_empty(self):
a = apply.Apply()
a.consensus = {}
consensus_file = os.path.join(data_dir, "empty.fasta")
self.assertRaises(AssertionError, a.load_consensus_file,
consensus_file)
def test_load_coordinates_file_empty(self):
a = apply.Apply()
a.coordinates = {}
coordinate_file = os.path.join(data_dir, "empty.coordinates")
self.assertRaises(json.JSONDecodeError, a.load_coordinates_file,
coordinate_file)
def test_load_coordinates_file_does_not_exist(self):
a = apply.Apply()
a.coordinates = {}
coordinate_file = os.path.join(data_dir, "doesnt_exist.coordinates")
self.assertRaises(AssertionError, a.load_coordinates_file,
coordinate_file)
def test_load_edits_in_range_no_coordinates(self):
a = apply.Apply()
edit_file = os.path.join(data_dir, "simple_edits")
self.assertRaises(AssertionError, a.load_edits_in_range, edit_file)
def test_load_input_files_missing_pair(self):
a = apply.Apply()
edit_file = os.path.join(data_dir, "all.edits")
missing_dir = os.path.join(data_dir, "missing_consensus")
self.assertRaises(AssertionError, a.load_input_files, missing_dir,
edit_file)
def test_load_consensus_file_no_consensus(self):
a = apply.Apply()
consensus_file = os.path.join(data_dir, "doesnt_exist.fasta")
self.assertRaises(AssertionError, a.load_consensus_file,
consensus_file)
