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)
