def test_create_configuration():
'Test default config'
fhand = NamedTemporaryFile()
fhand.write('[Snvs]\nmin_num_alleles = 2\n[[edge_removal]]\n454_left=None')
fhand.flush()
config_fpath = fhand.name
config = create_configuration(config_fpath)
assert config['Snvs']['min_quality'] == 45
#malformed
fhand = NamedTemporaryFile()
fhand.write('[blast]\n[[nr]]\nkind="nucl"\npath="path"\nspecies="all"')
fhand.flush()
config_fpath = fhand.name
config = create_configuration(config_fpath)
assert config['Snvs']['min_quality'] == 45
def do_analysis(kind, project_settings=None, analysis_config=None,
silent=False):
'It does one of the predefined analyses'
if project_settings is None:
project_settings = os.path.join(os.getcwd(),
BACKBONE_DIRECTORIES['config_file'])
if not os.path.exists(project_settings):
raise ValueError('Settings path not given and not found')
if not analysis_config:
analysis_config = {}
settings = create_configuration(project_settings)
specifications = get_analysis_especifications()
log_fpath = os.path.join(settings['General_settings']['project_path'],
BACKBONE_DIRECTORIES['log_file'])
_configure_logging(log_fpath, silent)
try:
analysis_def = specifications[kind]
except KeyError:
raise ValueError('Unknown analysis: ' + kind)
analyzer_klass = analysis_def['analyzer']
analyzer = analyzer_klass(project_settings=settings,
analysis_definition=analysis_def, silent=silent)
analyzer.run()
def test_create_project():
'We can create a project'
test_dir = NamedTemporaryDir()
settings_path = create_project(directory=test_dir.name,
name='backbone')
assert settings_path == join(test_dir.name,
'backbone', BACKBONE_DIRECTORIES['config_file'])
settings = create_configuration(settings_path)
assert settings['General_settings']['project_name'] == 'backbone'
project_path = join(test_dir.name, 'backbone')
assert settings['General_settings']['project_path'] == project_path
assert settings['Cleaning']['strip_n_percent'] == 2.0
content = open(settings_path).read()
assert 'strip_n_percent' in content
test_dir.close()
