def test__id_sequence_match_unacceptable_mismatch(self):
expected_name = "test_grna_2"
names_and_seqs = [("test_grna_1", "ACCG"),
(expected_name, "AAAT")]
matcher = GrnaPositionMatcher(names_and_seqs, 4)
output = matcher._id_sequence_match(1, "TTCA")
self.assertIsNone(output)
def test__id_sequence_match_unacceptable_mismatch(self):
expected_name = "test_grna_2"
names_and_seqs = [("test_grna_1", "ACCG"),
(expected_name, "AAAT")]
matcher = GrnaPositionMatcher(names_and_seqs, 4, 1, 1)
output = matcher._id_sequence_match(1, "TTCA")
self.assertIsNone(output)
def test__id_sequence_match_acceptable_mismatch(self):
expected_name = "test_grna_2"
names_and_seqs = [("test_grna_1", "ACCG"),
(expected_name, "AAAT")]
matcher = GrnaPositionMatcher(names_and_seqs, 4, 1, 1)
output = matcher._id_sequence_match(1, "AACT")
self.assertEqual(expected_name, output)
def test__id_pair_matches_neither(self):
name1 = "test_grna_1"
name2 = "test_grna_2"
names_and_seqs = [(name1, "ACCG"),
(name2, "AAAT")]
matcher = GrnaPositionMatcher(names_and_seqs, 4)
grnaA, grnaB = matcher._id_pair_matches("TTAA", "AGGG")
self.assertIsNone(grnaA)
self.assertIsNone(grnaB)
def test__id_pair_matches_both(self):
name1 = "test_grna_1"
name2 = "test_grna_2"
names_and_seqs = [(name1, "ACCG"),
(name2, "AAAT")]
matcher = GrnaPositionMatcher(names_and_seqs, 4)
grnaA, grnaB = matcher._id_pair_matches("AAAA", "ACCC")
self.assertEqual(name2, grnaA)
self.assertEqual(name1, grnaB)
def test__id_sequence_match_perfect(self):
expected_name = "test_grna_2"
test_seq = "AAAT"
names_and_seqs = [("test_grna_1", "ACCG"),
(expected_name, test_seq)]
matcher = GrnaPositionMatcher(names_and_seqs, 4)
output = matcher._id_sequence_match(1, test_seq)
self.assertEqual(expected_name, output)
def test__id_pair_matches_neither(self):
name1 = "test_grna_1"
name2 = "test_grna_2"
names_and_seqs = [(name1, "ACCG"),
(name2, "AAAT")]
matcher = GrnaPositionMatcher(names_and_seqs, 4, 1, 1)
grnaA, grnaB = matcher._id_pair_matches("TTAA", "AGGG")
self.assertIsNone(grnaA)
self.assertIsNone(grnaB)
def test__id_pair_matches_a_but_not_b(self):
name1 = "test_grna_1"
name2 = "test_grna_2"
names_and_seqs = [(name1, "ACCG"),
(name2, "AAAT")]
matcher = GrnaPositionMatcher(names_and_seqs, 4, 1, 1)
grnaA, grnaB = matcher._id_pair_matches("AAAA", "AGGG")
self.assertEqual(name2, grnaA)
self.assertIsNone(grnaB)
def test__id_pair_matches_both(self):
name1 = "test_grna_1"
name2 = "test_grna_2"
names_and_seqs = [(name1, "ACCG"),
(name2, "AAAT")]
matcher = GrnaPositionMatcher(names_and_seqs, 4, 1, 1)
grnaA, grnaB = matcher._id_pair_matches("AAAA", "ACCC")
self.assertEqual(name2, grnaA)
self.assertEqual(name1, grnaB)
def test__id_sequence_match_perfect(self):
expected_name = "test_grna_2"
test_seq = "AAAT"
names_and_seqs = [("test_grna_1", "ACCG"),
(expected_name, test_seq)]
matcher = GrnaPositionMatcher(names_and_seqs, 4, 1, 1)
output = matcher._id_sequence_match(1, test_seq)
self.assertEqual(expected_name, output)
def test_find_fw_and_rv_read_matches(self):
name2 = "test_grna_2"
name3 = "something_else"
names_and_seqs = [("test_grna_1", "ACCG"),
(name2, "AAAT"),
(name3, "GGAG")]
matcher = GrnaPositionMatcher(names_and_seqs, 4, 1, 1)
grnaA, grnaB = matcher.find_fw_and_rv_read_matches("AACT", "CTCA")
self.assertEqual(grnaA, name2)
self.assertEqual(grnaB, name3)
def test__match_and_count_constructs(self):
# 1: three; 2: two; 3: two; 4: none; 5: two; 6: one
fw_fastqs = """@D00611:278:HK55CBCXX:1:1101:1138:2170 1:N:0:ATCACG
ATGCAAGCTCATTGTGAAC
+
GGGGGGGIGGGGGIGAAGG
@D00611:278:HK55CBCXX:1:1101:1375:2236 1:N:0:ATCACG
TTCGGTACGAAACCAGCAC
+
GIIGIIIGGIIIIGIGIGG
@D00611:278:HK55CBCXX:1:1101:1360:2249 1:N:0:ATCACG
TTCGGTACGAAACCAGCAC
+
<<GGGGG<GGGGGGGGIGG
@D00611:278:HK55CBCXX:1:1101:1696:2177 1:N:0:ATCACC
CAACGGGCGTGCCCGGAAA
+
.G.<........<.<...<
@D00611:278:HK55CBCXX:1:1101:1532:2202 1:N:0:ATCACG
TTCGGTACGAAACCAGCAC
+
GIIGGGGGIIGIIIIIIIG
@D00611:278:HK55CBCXX:1:1101:1793:2194 1:N:0:ATCACG
TGTCTGGCCGCGAAGCAGT
+
IIIIIIIIIIIIIIIGIII
"""
# 1: two rc; 2: none; 3: one rc; 4: none; 5: one rc; 6: two rc
rv_fastqs = """@D00611:278:HK55CBCXX:1:1101:1138:2170 2:N:0:ATCACG
GTGCGGGTTTCGTACCGAA
+
GGIIGIIGGGGGAGAGGII
@D00611:278:HK55CBCXX:1:1101:1375:2236 2:N:0:ATCACG
TATGCCGGGACTAGAATGG
+
IIIGGGGIIIGGGGGIGII
@D00611:278:HK55CBCXX:1:1101:1360:2249 2:N:0:ATCACG
ACTGCTTCGCGGCCAGACA
+
IGGGGGAGGIGAGGGIGGA
@D00611:278:HK55CBCXX:1:1101:1696:2177 2:N:0:ATCACC
GACACCCAGGGAGCGCGCC
+
.<...<......<......
@D00611:278:HK55CBCXX:1:1101:1532:2202 2:N:0:ATCACG
ACTGCTTCGCGGCCAGACA
+
GIIIIIIAGIIIIIIIIII
@D00611:278:HK55CBCXX:1:1101:1793:2194 2:N:0:ATCACG
GTGCGGGTTTCGTACCGAA
+
GGIIIGIIGIIIIIIIIII
"""
fw_fastq_handler = FastqHandler(fw_fastqs, True)
rv_fastq_handler = FastqHandler(rv_fastqs, True)
grna_names_and_seqs = [
("one", "TGTCTGGCCGCGAAGCAGT"),
("two", "TTCGGTACGAAACCCGCAC"), # note one mismatch to fastq seq
("three", "ATGCAAGCTCATTGTGAAC")
]
construct_names = ["three__one", "two__one", "three__two"]
construct_counts = get_counter_from_names(construct_names)
grna_matcher = GrnaPositionMatcher(grna_names_and_seqs, 19, 1, 1)
output_construct_counts, output_summary_counts = _match_and_count_constructs(
grna_matcher, construct_counts, fw_fastq_handler, rv_fastq_handler)
self.assertEqual(3, len(output_construct_counts))
self.assertEqual(0, output_construct_counts["three__one"])
self.assertEqual(2, output_construct_counts["two__one"])
self.assertEqual(1, output_construct_counts["three__two"])
# also finds one instance of one__two, but this one is considered unrecognized as it isn't in the list of
# recognized construct names
self.assertEqual(5, len(output_summary_counts))
self.assertEqual(6, output_summary_counts["num_pairs"])
self.assertEqual(2, output_summary_counts["num_pairs_unrecognized"]
) # two, none and none, none
self.assertEqual(4, output_summary_counts["num_constructs_found"])
self.assertEqual(
1,
output_summary_counts["num_constructs_unrecognized"]) # one__two
self.assertEqual(3, output_summary_counts["num_constructs_recognized"])
def test__generate_seqs_to_check(self):
fw_output, rv_output = GrnaPositionMatcher._generate_seqs_to_check("ACCG", "AAAT")
self.assertEqual("ACCG", fw_output)
self.assertEqual("ATTT", rv_output)
def test__generate_seqs_to_check(self):
fw_output, rv_output = GrnaPositionMatcher._generate_seqs_to_check("ACCG", "AAAT")
self.assertEqual("ACCG", fw_output)
self.assertEqual("ATTT", rv_output)