def _make_seq_run():
"""
Make a sequencing run pointed at real data for the tests
:return: SequencingRun object
"""
files_1 = model.SequenceFile([
path.join(path_to_module, "fake_ngs_data", "Data", "Intensities",
"BaseCalls", "01-1111_S1_L001_R1_001.fastq.gz"),
path.join(path_to_module, "fake_ngs_data", "Data", "Intensities",
"BaseCalls", "01-1111_S1_L001_R2_001.fastq.gz"),
])
files_2 = model.SequenceFile([
path.join(path_to_module, "fake_ngs_data", "Data", "Intensities",
"BaseCalls", "02-2222_S1_L001_R1_001.fastq.gz"),
path.join(path_to_module, "fake_ngs_data", "Data", "Intensities",
"BaseCalls", "02-2222_S1_L001_R2_001.fastq.gz"),
])
files_3 = model.SequenceFile([
path.join(path_to_module, "fake_ngs_data", "Data", "Intensities",
"BaseCalls", "03-3333_S1_L001_R1_001.fastq.gz"),
path.join(path_to_module, "fake_ngs_data", "Data", "Intensities",
"BaseCalls", "03-3333_S1_L001_R2_001.fastq.gz"),
])
sample_1 = model.Sample("test_sample", "description", 1)
sample_1.sequence_file = files_1
sample_2 = model.Sample("test_sample", "description", 1)
sample_2.sequence_file = files_2
sample_3 = model.Sample("test_sample", "description", 1)
sample_3.sequence_file = files_3
project = model.Project("test_project", [sample_1, sample_2, sample_3],
"description")
sequencing_run = model.SequencingRun({"layoutType": "PAIRED_END"},
[project], "miseq")
return sequencing_run
def build_sequencing_run_from_samples(sample_sheet_file, metadata,
sequencing_run_type):
"""
Create a SequencingRun object with full project/sample/sequence_file structure
:param sample_sheet_file:
:param metadata:
:param sequencing_run_type:
:return: SequencingRun
"""
sample_list = _parse_sample_list(sample_sheet_file)
logging.debug("Building SequencingRun from parsed data")
# create list of projects and add samples to appropriate project
project_list = []
for sample in sample_list:
project = None
for p in project_list:
if sample.get('sample_project') == p.id:
project = p
if project is None:
project = model.Project(id=sample.get('sample_project'))
project_list.append(project)
project.add_sample(sample)
sequence_run = model.SequencingRun(metadata=metadata,
project_list=project_list,
sequencing_run_type=sequencing_run_type)
logging.debug("SequencingRun built")
return sequence_run
def build_sequencing_run_from_samples(sample_list, metadata,
sequence_run_type):
"""
Create a SequencingRun object with full project/sample/sequence_file structure
:param sample_list: List of Sample objects
:param metadata: metadata dict to add to the run
:param sequence_run_type: string identifier for sequencer type when generating api route
:return: SequencingRun
"""
logging.debug("Building SequencingRun from parsed data")
# create list of projects and add samples to appropriate project
project_list = []
for sample in sample_list:
project = None
for p in project_list:
if sample.get('sample_project') == p.id:
project = p
if project is None:
project = model.Project(id=sample.get('sample_project'))
project_list.append(project)
project.add_sample(sample)
sequence_run = model.SequencingRun(metadata=metadata,
project_list=project_list,
sequencing_run_type=sequence_run_type)
logging.debug("SequencingRun built")
return sequence_run