def test_view(self):
"""
Test the view method
"""
data = {
"profiles.csv": [{"PROJECTID": "ENCODE", "project_id": "ENCODE", "ANNOTATION": ""}],
"annotations.csv": [{}],
"genomes.csv": [],
"accessions.csv": [
{
"project_id": "ENCODE",
"accession_id": "ABCD",
"species": "H**o sapiens",
"cell": "cell",
"readType": "1x70D",
"type": "type",
"qualities": "qualities",
"dataType": "dataType",
"rnaExtract": "rnaExtract",
"localization": "localization",
"lab": "lab",
}
],
"runs.csv": [{"project_id": "ENCODE", "run_id": "run_id", "read_length": 70}],
"files.csv": [
{"project_id": "ENCODE", "accession_id": "ABCD", "type": "fastq", "file_location": "myfile.fastq.gz"}
],
}
view.main(data, SANDBOX)
def install(self):
workspace = self.buildout['extract']['workspace']
staging = self.options['staging']
if not os.path.exists(staging):
os.makedirs(staging)
data = {}
for source in [f for f in glob.glob(os.path.join(workspace, '*.csv'))]:
file_name = os.path.split(source)[-1]
target = os.path.join(staging, file_name)
shutil.copyfile(source, target)
data[file_name] = read_csv(target)
accessions.main(data, staging)
annotations.main(data, staging)
files.main(data, staging)
genomes.main(data, staging)
profiles.main(data)
experiments.main(data, staging)
read_length.main(data, staging)
view.main(data, staging)
def install(self):
workspace = self.buildout['extract']['workspace']
staging = self.options['staging']
if not os.path.exists(staging):
os.makedirs(staging)
data = {}
for source in [f for f in glob.glob(os.path.join(workspace, '*.csv'))]:
file_name = os.path.split(source)[-1]
target = os.path.join(staging, file_name)
shutil.copyfile(source, target)
data[file_name] = read_csv(target)
accessions.main(data, staging)
annotations.main(data, staging)
files.main(data, staging)
genomes.main(data, staging)
profiles.main(data)
experiments.main(data, staging)
read_length.main(data, staging)
view.main(data, staging)
def test_view(self):
"""
Test the view method
"""
data = {
'profiles.csv': [{
'PROJECTID': 'ENCODE',
'project_id': 'ENCODE',
'ANNOTATION': ''
}],
'annotations.csv': [{}],
'genomes.csv': [],
'accessions.csv': [{
'project_id': 'ENCODE',
'accession_id': 'ABCD',
'species': 'H**o sapiens',
'cell': 'cell',
'readType': '1x70D',
'type': 'type',
'qualities': 'qualities',
'dataType': 'dataType',
'rnaExtract': 'rnaExtract',
'localization': 'localization',
'lab': 'lab'
}],
'runs.csv': [{
'project_id': 'ENCODE',
'run_id': 'run_id',
'read_length': 70
}],
'files.csv': [{
'project_id': 'ENCODE',
'accession_id': 'ABCD',
'type': 'fastq',
'file_location': 'myfile.fastq.gz'
}],
}
view.main(data, SANDBOX)