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)