def test_get_clusters_from_fasta_filepath_extending_reference_db(self):
""" Correct clusters when clustering against db and adding new clusters
"""
clusters_res = get_clusters_from_fasta_filepath(
self.tmp_unsorted_fasta_filepath,
original_fasta_path=None,
max_accepts=7,
max_rejects=12,
percent_ID=0.90,
subject_fasta_filepath=self.ref_dna_seqs_fp,
suppress_new_clusters=False,
enable_rev_strand_matching=True,
HALT_EXEC=False,
save_uc_files=False)
self.ref_test_clusters2.sort()
self.ref_test_failures2.sort()
self.ref_test_new_seeds2.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,
(self.ref_test_clusters2, self.ref_test_failures2,
self.ref_test_new_seeds2))
def test_get_clusters_from_fasta_filepath_rev_strand_match(self):
""" Test OTUs from filepath functions with rev strand match
"""
# seq and its rc don't cluster when enable_rev_strand_matching = False
expected_cluster_list = [['uclust_test_seqs_0'],
['uclust_test_seqs_0_rc']]
expected_failure_list = []
expected_new_seed_list = [
'uclust_test_seqs_0', 'uclust_test_seqs_0_rc'
]
clusters_res = \
get_clusters_from_fasta_filepath(self.tmp_raw_dna_seqs_rc_filepath,
original_fasta_path = None, save_uc_files=False,
percent_ID = 0.90, enable_rev_strand_matching = False)
expected_cluster_list.sort()
expected_failure_list.sort()
expected_new_seed_list.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,
(expected_cluster_list, expected_failure_list,
expected_new_seed_list))
# seq and its rc cluster when enable_rev_strand_matching = False
expected_cluster_list = [[
'uclust_test_seqs_0', 'uclust_test_seqs_0_rc'
]]
expected_failure_list = []
expected_new_seed_list = ['uclust_test_seqs_0']
clusters_res = \
get_clusters_from_fasta_filepath(self.tmp_raw_dna_seqs_rc_filepath,
original_fasta_path = None, save_uc_files=False,
percent_ID = 0.90, enable_rev_strand_matching = True)
expected_cluster_list.sort()
expected_failure_list.sort()
expected_new_seed_list.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,
(expected_cluster_list, expected_failure_list,
expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_rev_strand_match(self):
""" Test OTUs from filepath functions with rev strand match
"""
# seq and its rc don't cluster when enable_rev_strand_matching = False
expected_cluster_list = [['uclust_test_seqs_0'], ['uclust_test_seqs_0_rc']]
expected_failure_list = []
expected_new_seed_list = ['uclust_test_seqs_0', 'uclust_test_seqs_0_rc']
clusters_res = \
get_clusters_from_fasta_filepath(self.tmp_raw_dna_seqs_rc_filepath,
original_fasta_path = None, save_uc_files=False,
percent_ID = 0.90, enable_rev_strand_matching = False)
expected_cluster_list.sort()
expected_failure_list.sort()
expected_new_seed_list.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,(expected_cluster_list,
expected_failure_list,
expected_new_seed_list))
# seq and its rc cluster when enable_rev_strand_matching = False
expected_cluster_list = [['uclust_test_seqs_0', 'uclust_test_seqs_0_rc']]
expected_failure_list = []
expected_new_seed_list = ['uclust_test_seqs_0']
clusters_res = \
get_clusters_from_fasta_filepath(self.tmp_raw_dna_seqs_rc_filepath,
original_fasta_path = None, save_uc_files=False,
percent_ID = 0.90, enable_rev_strand_matching = True)
expected_cluster_list.sort()
expected_failure_list.sort()
expected_new_seed_list.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,(expected_cluster_list,
expected_failure_list,
expected_new_seed_list))
def test_get_clusters_from_fasta_filepath(self):
""" Tests for return of lists of OTUs from given fasta filepath """
clusters_res = \
get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath, \
original_fasta_path = None, percent_ID = 0.90, save_uc_files=False)
expected_cluster_list.sort()
expected_failure_list.sort()
expected_new_seed_list.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,(expected_cluster_list,
expected_failure_list,
expected_new_seed_list))
def test_get_clusters_from_fasta_filepath(self):
""" Tests for return of lists of OTUs from given fasta filepath """
clusters_res = \
get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath, \
original_fasta_path = None, percent_ID = 0.90, save_uc_files=False)
expected_cluster_list.sort()
expected_failure_list.sort()
expected_new_seed_list.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,
(expected_cluster_list, expected_failure_list,
expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_optimal(self):
""" Test OTUs from filepath functions with optimal
"""
# need to compile a small test where optimal has an affect --
# this currently is only testing that we don't get a failure with
# optimal
clusters_res = \
get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath,
original_fasta_path = None, save_uc_files=False,
percent_ID = 0.90, optimal = True)
expected_cluster_list.sort()
expected_failure_list.sort()
expected_new_seed_list.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,(expected_cluster_list,
expected_failure_list,
expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_optimal(self):
""" Test OTUs from filepath functions with optimal
"""
# need to compile a small test where optimal has an affect --
# this currently is only testing that we don't get a failure with
# optimal
clusters_res = \
get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath,
original_fasta_path = None, save_uc_files=False,
percent_ID = 0.90, optimal = True)
expected_cluster_list.sort()
expected_failure_list.sort()
expected_new_seed_list.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,
(expected_cluster_list, expected_failure_list,
expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_suppress_sort(self):
""" Test OTUs from filepath functions with suppress sort
"""
expected = [['uclust_test_seqs_0'], ['uclust_test_seqs_1'],
['uclust_test_seqs_2'], ['uclust_test_seqs_3'],
['uclust_test_seqs_4'], ['uclust_test_seqs_5'],
['uclust_test_seqs_6', 'uclust_test_seqs_8'],
['uclust_test_seqs_7'], ['uclust_test_seqs_9']]
clusters_res = \
get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath,
original_fasta_path = None,
percent_ID = 0.90, suppress_sort = True, save_uc_files=False)
expected_cluster_list.sort()
expected_failure_list.sort()
expected_new_seed_list.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,(expected_cluster_list,
expected_failure_list,
expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_suppress_sort(self):
""" Test OTUs from filepath functions with suppress sort
"""
expected = [['uclust_test_seqs_0'], ['uclust_test_seqs_1'],
['uclust_test_seqs_2'], ['uclust_test_seqs_3'],
['uclust_test_seqs_4'], ['uclust_test_seqs_5'],
['uclust_test_seqs_6', 'uclust_test_seqs_8'],
['uclust_test_seqs_7'], ['uclust_test_seqs_9']]
clusters_res = \
get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath,
original_fasta_path = None,
percent_ID = 0.90, suppress_sort = True, save_uc_files=False)
expected_cluster_list.sort()
expected_failure_list.sort()
expected_new_seed_list.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,
(expected_cluster_list, expected_failure_list,
expected_new_seed_list))
def test_get_clusters_from_fasta_filepath_extending_reference_db(self):
""" Correct clusters when clustering against db and adding new clusters
"""
clusters_res = get_clusters_from_fasta_filepath(
self.tmp_unsorted_fasta_filepath,
original_fasta_path = None,
max_accepts=7,max_rejects=12,
percent_ID = 0.90,
subject_fasta_filepath=self.ref_dna_seqs_fp,
suppress_new_clusters=False,enable_rev_strand_matching=True,
HALT_EXEC=False,
save_uc_files=False)
self.ref_test_clusters2.sort()
self.ref_test_failures2.sort()
self.ref_test_new_seeds2.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,(self.ref_test_clusters2,
self.ref_test_failures2,
self.ref_test_new_seeds2))
def test_get_clusters_from_fasta_filepath_reference_db_only(self):
""" Correct clusters returned when clustering against a database only
"""
clusters_res = get_clusters_from_fasta_filepath(
self.tmp_unsorted_fasta_filepath,
original_fasta_path = None,
save_uc_files=False,
max_accepts=7,max_rejects=12,
percent_ID = 0.90,
subject_fasta_filepath=self.ref_dna_seqs_fp,
suppress_new_clusters=True,
HALT_EXEC=False)
self.ref_test_clusters1.sort()
self.ref_test_failures1.sort()
self.ref_test_new_seeds1.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,(self.ref_test_clusters1,
self.ref_test_failures1,
self.ref_test_new_seeds1))
def test_get_clusters_from_fasta_filepath_reference_db_only(self):
""" Correct clusters returned when clustering against a database only
"""
clusters_res = get_clusters_from_fasta_filepath(
self.tmp_unsorted_fasta_filepath,
original_fasta_path=None,
save_uc_files=False,
max_accepts=7,
max_rejects=12,
percent_ID=0.90,
subject_fasta_filepath=self.ref_dna_seqs_fp,
suppress_new_clusters=True,
HALT_EXEC=False)
self.ref_test_clusters1.sort()
self.ref_test_failures1.sort()
self.ref_test_new_seeds1.sort()
clusters_res[0].sort()
clusters_res[1].sort()
clusters_res[2].sort()
self.assertEqual(clusters_res,
(self.ref_test_clusters1, self.ref_test_failures1,
self.ref_test_new_seeds1))
