def test_experiments(self):
"""
Test the experiments method
"""
data = {
"accessions.csv": [
{
"project_id": "ENCODE",
"accession_id": "ABCD",
"species": "H**o sapiens",
"cell": "cell",
"readType": "readType",
"type": "type",
"qualities": "qualities",
"dataType": "dataType",
"rnaExtract": "rnaExtract",
"localization": "localization",
"lab": "lab",
}
]
}
experiments.main(data, SANDBOX)
file_path = os.path.join(SANDBOX, "experiments.csv")
file_content = open(file_path, "r").read()
header = "\t".join(["project_id", "accession_id", "replicate_id"])
line = "\t".join(["ENCODE", "ABCD", "1"])
expected = "%s\n%s\n" % (header, line)
self.failUnless(file_content == expected, file_content)
def test_experiments(self):
"""
Test the experiments method
"""
data = {
'accessions.csv': [{
'project_id': 'ENCODE',
'accession_id': 'ABCD',
'species': 'H**o sapiens',
'cell': 'cell',
'readType': 'readType',
'type': 'type',
'qualities': 'qualities',
'dataType': 'dataType',
'rnaExtract': 'rnaExtract',
'localization': 'localization',
'lab': 'lab'
}]
}
experiments.main(data, SANDBOX)
file_path = os.path.join(SANDBOX, 'experiments.csv')
file_content = open(file_path, 'r').read()
header = "\t".join(['project_id', 'accession_id', 'replicate_id'])
line = "\t".join(['ENCODE', 'ABCD', '1'])
expected = "%s\n%s\n" % (header, line)
self.failUnless(file_content == expected, file_content)
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)
