def test_calculate_accession_coverage_rounding_error(self):
accession_data = {
"total_length": 545,
"contigs": ["CONTIG_1"],
"reads": [],
}
contig_data = {
"CONTIG_1": {
"total_length": 400,
"accession": "ACCESSION_1",
"query_start": 320,
"query_end": 322,
"subject_start": 221,
"subject_end": 219,
"coverage": [1] * 400
}
}
read_data = {}
(coverage, bin_size
) = PipelineStepGenerateCoverageViz.calculate_accession_coverage(
"ACCESSION_1", accession_data, contig_data, read_data, 500)
self.assertEqual(coverage,
[[200, 1.0, 1.0, 1, 0], [201, 1.0, 1.0, 1, 0],
[202, 0.75, 0.752, 1, 0]])
self.assertEqual(bin_size, 1.09)
def test_calculate_accession_coverage_multiple_reads(self):
accession_data = {
"total_length": 10,
"contigs": [],
"reads": ["READS_1", "READS_2"]
}
contig_data = {}
read_data = {
"READS_1": {
"accession": "ACCESSION_1",
"subject_start": 4,
"subject_end": 7,
},
"READS_2": {
"accession": "ACCESSION_1",
"subject_start": 6,
"subject_end": 9,
}
}
(coverage, bin_size
) = PipelineStepGenerateCoverageViz.calculate_accession_coverage(
"ACCESSION_1", accession_data, contig_data, read_data, 10)
self.assertEqual(coverage, [
[3, 1.0, 1, 0, 1],
[4, 1.0, 1, 0, 1],
[5, 2.0, 1, 0, 2],
[6, 2.0, 1, 0, 2],
[7, 1.0, 1, 0, 1],
[8, 1.0, 1, 0, 1],
])
self.assertEqual(bin_size, 1)
def test_calculate_accession_coverage_max_bins_small(self):
accession_data = {
"total_length": 10,
"contigs": ["CONTIG_1"],
"reads": []
}
contig_data = {
"CONTIG_1": {
"total_length": 6,
"accession": "ACCESSION_1",
"query_start": 1,
"query_end": 4,
"subject_start": 4,
"subject_end": 7,
"coverage": [1, 2, 3, 4, 5, 6]
}
}
read_data = {}
(coverage, bin_size
) = PipelineStepGenerateCoverageViz.calculate_accession_coverage(
"ACCESSION_1", accession_data, contig_data, read_data, 5)
# The coverage is reduced (e.g. divided by 2) for bins with 0.5 and 2.0.
# Since the contig only covers half of that bin.
self.assertEqual(coverage, [
[1, 0.5, 0.5, 1, 0],
[2, 2.5, 1, 1, 0],
[3, 2.0, 0.5, 1, 0],
])
self.assertEqual(bin_size, 2)
def test_calculate_accession_coverage_offset_varying_reverse(self):
accession_data = {
"total_length": 10,
"contigs": ["CONTIG_1"],
"reads": []
}
contig_data = {
"CONTIG_1": {
"total_length": 5,
"accession": "ACCESSION_1",
"query_start": 1,
"query_end": 5,
"subject_start": 9,
"subject_end": 3,
"coverage": [1, 2, 3, 4, 5]
}
}
read_data = {}
(coverage, bin_size
) = PipelineStepGenerateCoverageViz.calculate_accession_coverage(
"ACCESSION_1", accession_data, contig_data, read_data, 10)
self.assertEqual(coverage, [
[2, 5.0, 1, 1, 0],
[3, 4.5, 1, 1, 0],
[4, 3.5, 1, 1, 0],
[5, 3.0, 1, 1, 0],
[6, 2.5, 1, 1, 0],
[7, 1.5, 1, 1, 0],
[8, 1.0, 1, 1, 0],
])
self.assertEqual(bin_size, 1.0)
def test_calculate_accession_coverage_partial_contig(self):
accession_data = {
"total_length": 10,
"contigs": ["CONTIG_1"],
"reads": []
}
contig_data = {
"CONTIG_1": {
"total_length": 7,
"accession": "ACCESSION_1",
"query_start": 1,
"query_end": 7,
"subject_start": 3,
"subject_end": 9,
"coverage": [2] * 6, # Coverage is 6 instead of 7.
}
}
read_data = {}
(coverage, bin_size
) = PipelineStepGenerateCoverageViz.calculate_accession_coverage(
"ACCESSION_1", accession_data, contig_data, read_data, 10)
self.assertEqual(coverage, [
[2, 2.0, 1, 1, 0],
[3, 2.0, 1, 1, 0],
[4, 2.0, 1, 1, 0],
[5, 2.0, 1, 1, 0],
[6, 2.0, 1, 1, 0],
[7, 2.0, 1, 1, 0],
[8, 2.0, 1, 1, 0],
])
self.assertEqual(bin_size, 1.0)
def test_calculate_accession_coverage_basic(self):
accession_data = {
"total_length": 4,
"contigs": ["CONTIG_1"],
"reads": []
}
contig_data = {
"CONTIG_1": {
"total_length": 4,
"accession": "ACCESSION_1",
"query_start": 1,
"query_end": 4,
"subject_start": 1,
"subject_end": 4,
"coverage": [2] * 4,
}
}
read_data = {}
(coverage, bin_size
) = PipelineStepGenerateCoverageViz.calculate_accession_coverage(
"ACCESSION_1", accession_data, contig_data, read_data, 4)
self.assertEqual(coverage, [
[0, 2.0, 1, 1, 0],
[1, 2.0, 1, 1, 0],
[2, 2.0, 1, 1, 0],
[3, 2.0, 1, 1, 0],
])
self.assertEqual(bin_size, 1.0)
def test_calculate_accession_coverage_max_bins_small_reads(self):
accession_data = {
"total_length": 10,
"contigs": ["CONTIG_1"],
"reads": ["READS_1", "READS_2"]
}
contig_data = {
"CONTIG_1": {
"total_length": 6,
"accession": "ACCESSION_1",
"query_start": 3,
"query_end": 4,
"subject_start": 6,
"subject_end": 7,
"coverage": [1, 2, 3, 4, 5, 6]
}
}
read_data = {
"READS_1": {
"accession": "ACCESSION_1",
"subject_start": 2,
"subject_end": 3,
},
"READS_2": {
"accession": "ACCESSION_1",
"subject_start": 10,
"subject_end": 10,
}
}
(coverage, bin_size
) = PipelineStepGenerateCoverageViz.calculate_accession_coverage(
"ACCESSION_1", accession_data, contig_data, read_data, 5)
# [0.5, 0.5] from READS_1.
# [1.5, 2.0] from CONTIG_1
# last [0.5] from READS_2.
self.assertEqual(coverage, [
[0, 0.5, 0.5, 0, 1],
[1, 0.5, 0.5, 0, 1],
[2, 1.5, 0.5, 1, 0],
[3, 2.0, 0.5, 1, 0],
[4, 0.5, 0.5, 0, 1],
])
self.assertEqual(bin_size, 2)
def test_calculate_accession_coverage_max_bins(self):
accession_data = {
"total_length": 10,
"contigs": ["CONTIG_1"],
"reads": []
}
contig_data = {
"CONTIG_1": {
"total_length": 5,
"accession": "ACCESSION_1",
"query_start": 1,
"query_end": 5,
"subject_start": 1,
"subject_end": 10,
"coverage": [2.0] * 5
}
}
read_data = {}
(coverage, bin_size
) = PipelineStepGenerateCoverageViz.calculate_accession_coverage(
"ACCESSION_1", accession_data, contig_data, read_data, 9)
self.assertEqual(coverage, [
[0, 2.0, 1, 1, 0],
[1, 2.0, 1, 1, 0],
[2, 2.0, 1, 1, 0],
[3, 2.0, 1, 1, 0],
[4, 2.0, 1, 1, 0],
[5, 2.0, 1, 1, 0],
[6, 2.0, 1, 1, 0],
[7, 2.0, 1, 1, 0],
[8, 2.0, 1, 1, 0],
])
self.assertTrue((bin_size - 10 / 9) < 0.01)