def test_three_contig_1(self):
c_1 = ['GATCTTTT', 'GATCGATC','ATCAAAAA']
contig_dict_1 = mc.merge_check_global(c_1, 3)
bbr_test_1 = mc.suffix_filter(contig_dict_1)
bbr_truth_1 = {'GATCGATC':['GATCTTTT', 4]}
self.assertEqual(bbr_test_1,bbr_truth_1)
c_2 = ['GATCAAAA', 'CCCGGAAA','AAAAGATC']
contig_dict_2 = mc.merge_check_global(c_2, 3)
bbr_test_2 = mc.suffix_filter(contig_dict_2)
bbr_truth_2 = {'CCCGGAAA':['AAAAGATC', 3], 'AAAAGATC':['GATCAAAA', 4], 'GATCAAAA':['AAAAGATC', 4]}
self.assertEqual(bbr_test_2,bbr_truth_2)
def test_three_contig_1(self):
c_1 = ['GATCTTTT', 'GATCGATC', 'ATCAAAAA']
contig_dict_1 = mc.merge_check_global(c_1, 3)
bbr_test_1 = mc.suffix_filter(contig_dict_1)
bbr_truth_1 = {'GATCGATC': ['GATCTTTT', 4]}
self.assertEqual(bbr_test_1, bbr_truth_1)
c_2 = ['GATCAAAA', 'CCCGGAAA', 'AAAAGATC']
contig_dict_2 = mc.merge_check_global(c_2, 3)
bbr_test_2 = mc.suffix_filter(contig_dict_2)
bbr_truth_2 = {
'CCCGGAAA': ['AAAAGATC', 3],
'AAAAGATC': ['GATCAAAA', 4],
'GATCAAAA': ['AAAAGATC', 4]
}
self.assertEqual(bbr_test_2, bbr_truth_2)
def test_read_updates_1(self):
c_1 = ['AAAATCA', 'AATCAGG', 'TTTTTTT']
contig_dict_1 = mc.merge_check_global(c_1, 3)
bbr_test_1 = mc.suffix_filter(contig_dict_1)
bbl_test_1 = mc.extract_bbl(bbr_test_1)
contig_trace_test_1 = mc.trace_contigs(bbl_test_1)
new_contigs_test_1 = mc.merge_contigs(contig_trace_test_1, c_1[:])
reads_dict_1 = {
'AAAAT': [[0, 0, 0.5, 1]],
'AAATC': [[0, 1, 0.5, 1]],
'AATCA': [[0, 2, 0.5, 1], [1, 0, 0.5, 1]],
'ATCAG': [[1, 1, 0.5, 1]],
'TTTTT': [[2, 0, 0.5, 1]]
}
reverse_dict_test_1 = mc.reverse_reads_dict(reads_dict_1)
new_reads_dict_test_1 = mc.change_reads_on_merge(
reverse_dict_test_1, reads_dict_1, contig_trace_test_1, c_1,
new_contigs_test_1)
new_reads_dict_truth_1 = {
'ATCAG': [[0, 3, 0.5, 1]],
'AATCA': [[0, 2, 0.5, 1]],
'AAAAT': [[0, 0, 0.5, 1]],
'TTTTT': [[1, 0, 0.5, 1]],
'AAATC': [[0, 1, 0.5, 1]]
}
self.assertEqual(new_reads_dict_truth_1, new_reads_dict_test_1)
def test_three_contig_2(self):
c_1 = ['GATCAAAA', 'CCCGGAAA','AAAAGATC']
contig_dict_1 = mc.merge_check_global(c_1, 3)
bbr_test_1 = mc.suffix_filter(contig_dict_1)
bbl_test_1 = mc.extract_bbl(bbr_test_1)
bbl_truth_1 = {'AAAAGATC':['GATCAAAA', 4], 'GATCAAAA':['AAAAGATC',4]}
self.assertEqual(bbl_test_1, bbl_truth_1)
def test_merge_check_1(self):
c_1 = ['GATCTTTT', 'GATCGATC']
test_1 = mc.merge_check_global(c_1, 3)
truth_1 = {
'GATCTTTT': Counter({'GATCGATC': 0}),
'GATCGATC': Counter({'GATCTTTT': 4})
}
self.assertEqual(test_1, truth_1)
def test_three_contig_3(self):
c_1 = ['GATCTAAA', 'CCCGAAAA','AAAAGATC']
contig_dict_1 = mc.merge_check_global(c_1, 3)
bbr_test_1 = mc.suffix_filter(contig_dict_1)
bbl_test_1 = mc.extract_bbl(bbr_test_1)
contig_trace_test_1 = mc.trace_contigs(bbl_test_1)
contig_trace_truth_1 = [[['CCCGAAAA',0],['AAAAGATC',4],['GATCTAAA',4]]]
self.assertEqual(contig_trace_test_1, contig_trace_truth_1)
def test_three_contig_4(self):
c_1 = ['GATCTAAA', 'CCCGAAAA', 'AAAAGATC']
contig_dict_1 = mc.merge_check_global(c_1, 3)
bbr_test_1 = mc.suffix_filter(contig_dict_1)
bbl_test_1 = mc.extract_bbl(bbr_test_1)
contig_trace_test_1 = mc.trace_contigs(bbl_test_1)
new_contigs_test_1 = mc.merge_contigs(contig_trace_test_1, c_1)
new_contigs_truth_1 = ['CCCGAAAAGATCTAAA']
self.assertEqual(new_contigs_test_1, new_contigs_truth_1)
def test_three_contig_2(self):
c_1 = ['GATCAAAA', 'CCCGGAAA', 'AAAAGATC']
contig_dict_1 = mc.merge_check_global(c_1, 3)
bbr_test_1 = mc.suffix_filter(contig_dict_1)
bbl_test_1 = mc.extract_bbl(bbr_test_1)
bbl_truth_1 = {
'AAAAGATC': ['GATCAAAA', 4],
'GATCAAAA': ['AAAAGATC', 4]
}
self.assertEqual(bbl_test_1, bbl_truth_1)
def test_read_updates_1(self):
c_1 = ['AAAATCA', 'AATCAGG', 'TTTTTTT']
contig_dict_1 = mc.merge_check_global(c_1,3)
bbr_test_1 = mc.suffix_filter(contig_dict_1)
bbl_test_1 = mc.extract_bbl(bbr_test_1)
contig_trace_test_1 = mc.trace_contigs(bbl_test_1)
new_contigs_test_1 = mc.merge_contigs(contig_trace_test_1, c_1[:])
reads_dict_1 = {'AAAAT':[[0,0,0.5,1]],'AAATC':[[0,1,0.5,1]],'AATCA':[[0,2,0.5,1],[1,0,0.5,1]],'ATCAG':[[1,1,0.5,1]],'TTTTT':[[2,0,0.5,1]]}
reverse_dict_test_1 = mc.reverse_reads_dict(reads_dict_1)
new_reads_dict_test_1 = mc.change_reads_on_merge(reverse_dict_test_1, reads_dict_1, contig_trace_test_1, c_1, new_contigs_test_1)
new_reads_dict_truth_1 = {'ATCAG': [[0,3,0.5,1]], 'AATCA': [[0,2,0.5,1]], 'AAAAT': [[0,0,0.5,1]], 'TTTTT': [[1,0,0.5,1]], 'AAATC': [[0,1,0.5,1]]}
self.assertEqual(new_reads_dict_truth_1, new_reads_dict_test_1)
def test_merge_check_2(self):
c_1 = ['GATCTTTT', 'GATCGATC']
test_1 = mc.merge_check_global(c_1, 5)
truth_1 = []
self.assertEqual(test_1, truth_1)
def test_merge_check_2(self):
c_1 = ['GATCTTTT', 'GATCGATC']
test_1 = mc.merge_check_global(c_1, 5)
truth_1 = []
self.assertEqual(test_1, truth_1)
def test_merge_check_1(self):
c_1 = ['GATCTTTT', 'GATCGATC']
test_1 = mc.merge_check_global(c_1, 3)
truth_1 = {'GATCTTTT': Counter({'GATCGATC':0}), 'GATCGATC': Counter({'GATCTTTT':4})}
self.assertEqual(test_1, truth_1)
