def test_calculate_accession_stats_basic(self):
accession_data = {
"total_length": 10,
"contigs": ["CONTIG_1"],
"reads": []
}
contig_data = {
"CONTIG_1": {
"total_length": 10,
"accession": "ACCESSION_1",
"query_start": 1,
"query_end": 10,
"subject_start": 1,
"subject_end": 10,
"coverage": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
"prop_mismatch": 0.1
}
}
read_data = {}
stats = PipelineStepGenerateCoverageViz.calculate_accession_stats(
accession_data, contig_data, {})
self.assertEqual(stats["max_aligned_length"], 10)
self.assertEqual(stats["coverage_depth"], 5.5)
self.assertEqual(stats["coverage_breadth"], 1)
self.assertEqual(stats["avg_prop_mismatch"], 0.1)
def test_calculate_accession_stats_multiple(self):
accession_data = {
"total_length": 100,
"contigs": ["CONTIG_1", "CONTIG_2"],
"reads": ["READ_1", "READ_2"]
}
contig_data = {
"CONTIG_1": {
"total_length": 100,
"accession": "ACCESSION_1",
"query_start": 1,
"query_end": 40,
"subject_start": 1,
"subject_end": 40,
"coverage": [2] * 40,
"prop_mismatch": 0.01
},
"CONTIG_2": {
"total_length": 100,
"accession": "ACCESSION_1",
"query_start": 1,
"query_end": 20,
"subject_start": 100,
"subject_end": 81,
"coverage": [4] * 20,
"prop_mismatch": 0.02
}
}
read_data = {
"READ_1": {
"total_length": 20,
"accession": "ACCESSION_1",
"query_start": 1,
"query_end": 20,
"subject_start": 1,
"subject_end": 20,
"prop_mismatch": 0.03
},
"READ_2": {
"total_length": 20,
"accession": "ACCESSION_1",
"query_start": 1,
"query_end": 20,
"subject_start": 100,
"subject_end": 81,
"prop_mismatch": 0.04
}
}
stats = PipelineStepGenerateCoverageViz.calculate_accession_stats(
accession_data, contig_data, read_data)
self.assertEqual(stats["max_aligned_length"], 40)
self.assertEqual(stats["coverage_depth"], 2)
self.assertEqual(stats["coverage_breadth"], 0.6)
self.assertEqual(stats["avg_prop_mismatch"], 0.025)