def create_experiment(
bam,
bedfile="/a/fake/bedfile",
assembly="GRCh37",
raw_data=None,
method="TD",
species="HUMAN",
category=None,
technique_name=None,
sample=None,
):
"""Easily create an experiment for testing purposes."""
# create technique
technique = factories.TechniqueFactory(method=method,
name=technique_name
or str(uuid.uuid4()))
# create experiment
bed_file_dict = dict(url=bedfile, description="")
technique["reference_data"][f"{assembly}_targets_bedfile"] = bed_file_dict
technique["reference_data"][f"{assembly}_baits_bedfile"] = bed_file_dict
experiment = factories.ExperimentFactory(technique=technique)
# force sample if provided
if sample: # pragma: no cover
experiment["sample"] = sample
else:
category = category or experiment["sample"]["category"]
experiment["sample"]["individual"]["species"] = species
experiment["sample"]["category"] = category
experiment["raw_data"] = raw_data or []
experiment["bam_files"][assembly] = dict(url=bam, analysis=1)
return api.create_instance("experiments", **experiment)
def test_get_bed():
runner = CliRunner()
technique = api.create_instance("techniques",
**factories.TechniqueFactory())
args = [str(technique.pk)]
result = runner.invoke(commands.get_bed, args, catch_exceptions=False)
assert "No BED files" in result.output
api.patch_instance(
"techniques",
technique.pk,
reference_data={"test_targets_bedfile": {
"url": "/hello/world"
}},
)
result = runner.invoke(commands.get_bed, args, catch_exceptions=False)
assert "/hello/world" in result.output
api.patch_instance(
"techniques",
technique.pk,
reference_data={
"test_targets_bedfile": {
"url": "/hello/world"
},
"another_targets_bedfile": {
"url": "/hello/world"
},
},
)
result = runner.invoke(commands.get_bed, args, catch_exceptions=False)
assert "Multiple BEDs" in result.output
def test_get_instances():
technique = api.create_instance("techniques",
**factories.TechniqueFactory())
assert api.get_instances("techniques",
[technique.name])[0].pk == technique.pk
experiment = api.create_instance("experiments",
**factories.ExperimentFactory())
individual = experiment.sample.individual
project = experiment.projects[0]
assert api.get_experiments([experiment.pk])[0].pk == experiment.pk
assert api.get_projects([project.pk])[0].pk == project.pk
assert api.get_tree(individual.pk).pk == individual.pk
assert api.get_trees([individual.pk])[0].pk == individual.pk
def test_import_bedfiles(tmpdir):
technique = api.create_instance("techniques",
**factories.TechniqueFactory())
targets = tmpdir.join("targets.bed")
baits = tmpdir.join("baits.bed")
targets.write("2\t1\t2\n1\t1\t2\n")
baits.write("2\t1\t2\n1\t1\t2\n")
species = "HUMAN"
runner = CliRunner()
technique = data.LocalBedImporter.import_bedfiles(
species=species,
technique=technique["pk"],
targets_path=targets.strpath,
baits_path=baits.strpath,
assembly="AnAssembly",
description="these are test BED files",
)
for i in "targets", "baits":
bedfile = technique["reference_data"][f"AnAssembly_{i}_bedfile"]["url"]
assert os.path.isfile(bedfile)
assert os.path.isfile(bedfile + ".tbi")
assert os.path.isfile(bedfile.replace(".gz", ""))
args = [str(technique.pk), "--bed-type", i]
result = runner.invoke(commands.get_bed, args, catch_exceptions=False)
assert bedfile in result.output
with open(bedfile.replace(".gz", ""), "r") as f: # test bed is sorted
assert next(f).startswith("1")
command = data.LocalBedImporter.as_cli_command()
args = [
"--targets-path",
targets.strpath,
"--baits-path",
baits.strpath,
"--technique",
technique["pk"],
"--assembly",
"AnAssembly",
"--species",
species,
"--description",
"Test",
]
result = runner.invoke(command, args, catch_exceptions=False)
assert "has registered BED files for" in result.output
def create_pair(
tumor_bam,
normal_bam,
bedfile="/a/fake/bedfile",
assembly="GRCh37",
method="TD",
species="HUMAN",
):
"""Create pair."""
pair = []
bed_file_dict = dict(url=bedfile, description="")
technique = factories.TechniqueFactory(method=method)
technique["reference_data"][f"{assembly}_targets_bedfile"] = bed_file_dict
technique["reference_data"][f"{assembly}_baits_bedfile"] = bed_file_dict
for (i, category) in [(tumor_bam, "TUMOR"), (normal_bam, "NORMAL")]:
experiment = factories.ExperimentFactory(technique=technique)
experiment["sample"]["individual"]["species"] = species
experiment["sample"]["category"] = category
experiment["bam_files"][assembly] = dict(url=i, analysis=1)
pair.append(api.create_instance("experiments", **experiment))
return pair[0], pair[1]