def align_reads(self, single_ref, test_seq): """ ALign Reads :param single_ref: :param test_seq: :return: """ aligned = ar.AlignedReads() aligned.align_reads_to_ref(test_seq, single_ref, 21) return aligned
def test_srna_profile_1(self): """ Test a single read aligning a reference once in the sense orientation """ test_seq = self.load_test_read_file() single_ref = self.load_test_ref_file("test_ref_1.fa") aligned = self.align_reads(single_ref, test_seq) test_aligned = ar.AlignedReads() test_aligned[dna.DNA("ATGCGTATGGCGATGAGAGTA")] = [[0, 500000.0]] self.assertEqual(aligned, test_aligned)
def test_srna_profile_5(self): """ Test a single read aligning a reference twice in the sense orientation Split of aligned read count """ test_seq = self.load_test_read_file() single_ref = self.load_test_ref_file("test_ref_4.fa") aligned = self.align_reads(single_ref, test_seq) aligned.split() test_aligned = ar.AlignedReads() test_aligned[dna.DNA("ATGCGTATGGCGATGAGAGTA")] = [[0, 250000.0], [27, 250000.0]] self.assertEqual(aligned, test_aligned)
def test_srna_profile_3(self): """ Test 2 reads aligning to the same reference once - 1 sense and 1 anti-sense :return: """ test_seq = self.load_test_read_file() single_ref = self.load_test_ref_file("test_ref_3.fa") aligned = self.align_reads(single_ref, test_seq) test_aligned = ar.AlignedReads() test_aligned[dna.DNA("GTGCGTATGGCGATGAGAGTA")] = [[47, -250000.0]] test_aligned[dna.DNA("ATGCGTATGGCGATGAGAGTA")] = [[0, 500000.0]] self.assertEqual(aligned, test_aligned)