def setUp(self): self.config = ProjectConfig() self.defaultJsonIO = StringIO("""\ { "projects": { "R1": { "max_variants": 0, "regions": [ { "coordinate_region": "R1", "coordinate_region_length": 3, "key_positions": [], "min_coverage1": 10, "min_coverage2": 50, "min_coverage3": 100, "seed_region_names": [ "R1-seed" ] } ] }, "R1 and R2": { "max_variants": 0, "regions": [ { "coordinate_region": "R1", "coordinate_region_length": 3, "key_positions": [1, 3], "min_coverage1": 10, "min_coverage2": 50, "min_coverage3": 100, "seed_region_names": [ "R1-seed" ] }, { "coordinate_region": "R2", "coordinate_region_length": 1, "key_positions": [], "min_coverage1": 10, "min_coverage2": 50, "min_coverage3": 100, "seed_region_names": [ "R2-seed" ] } ] } } } """)
def build_config(project, sequences): projects = ProjectConfig() projects.config = { 'projects': { project: { 'regions': [ { 'seed_region_names': list(sequences.keys()) } ] } }, 'regions': {name: {'reference': [sequence]} for name, sequence in sequences.items()} } return projects
def setUp(self): self.projects = ProjectConfig() self.projects.load( StringIO("""\ { "regions": { "R1-seed": { "seed_group": "main", "reference": ["ACTAAAGGG"] }, "R2-seed": { "seed_group": "main", "reference": ["ACTAAAGGGAAA"] } } } """)) self.sam_file = StringIO() self.remap_counts = StringIO() self.remap_counts_writer = DictWriter( self.remap_counts, ['type', 'filtered_count', 'count'], lineterminator=os.linesep) self.remap_counts_writer.writeheader()
def setUp(self): self.defaultJsonIO = StringIO("""\ { "projects": { "R1": { "max_variants": 5, "regions": [ { "coordinate_region": "R1", "seed_region_names": ["R1-seed"], "id": 10042 } ] } }, "regions": { "R1-seed": { "is_nucleotide": true, "reference": [ "ACTGAAA", "GGG" ], "seed_group": "R1-seeds" }, "R1": { "is_nucleotide": false, "reference": [ "RWN", "NWR" ], "seed_group": null } } } """) self.config = ProjectConfig()
def setUp(self): self.addTypeEqualityFunc(str, self.assertMultiLineEqual) config_json = StringIO("""\ { "projects": { "R1": { "max_variants": 0, "regions": [ { "coordinate_region": "R1", "coordinate_region_length": 3, "key_positions": [], "min_coverage1": 10, "min_coverage2": 50, "min_coverage3": 100, "seed_region_names": [ "R1-seed" ] } ] }, "R1-and-R2": { "max_variants": 0, "regions": [ { "coordinate_region": "R1", "coordinate_region_length": 3, "key_positions": [ { "end_pos": null, "start_pos": 1 }, { "end_pos": null, "start_pos": 3 } ], "min_coverage1": 10, "min_coverage2": 50, "min_coverage3": 100, "seed_region_names": [ "R1-seed" ] }, { "coordinate_region": "R2", "coordinate_region_length": 1, "key_positions": [], "min_coverage1": 10, "min_coverage2": 50, "min_coverage3": 100, "seed_region_names": [ "R2-seed" ] } ] } } } """) self.config = ProjectConfig() self.config.load(config_json)