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)