def init(context, setup, reset, automate):
"""Walk user through setting up a new config file."""
# print a nice welcome message
click.echo(chanjo.__banner__)
cov_tresholds = (context.obj.get('sambamba', {})
.get('cov_treshold', [10, 20]))
defaults = {'sambamba.cov_treshold': {'value': cov_tresholds,
'prompt': 'sufficient coverage'},
'database': {'value': context.obj['database'],
'prompt': 'central database path/URI'}}
if not automate:
questions = [(key, value['prompt'], value['value'])
for key, value in iteritems(defaults)]
# launch init pipeline
init_pipeline('chanjo', context.obj, questions)
else:
logger.info('setting default config values')
for key, value in iteritems(defaults):
context.obj.set(key, value['value'], scope=context.obj.user_data)
# write to the config file
context.obj.save(default_flow_style=False)
if setup:
chanjo_db = Store(uri=context.obj.user_data['database'])
if reset:
chanjo_db.tear_down()
chanjo_db.set_up()
class TestSambamba:
def setup(self):
self.store = Store('sqlite://')
self.store.set_up()
self.row_data = parse_sambamba.depth_output(bed_lines)
def teardown(self):
self.store.tear_down()
self.store.session.close()
def test_connection(self):
self.store.dialect == 'sqlite'
def test_rows(self):
stats = load_sambamba.rows(self.store.session, self.row_data)
all_stats = [stat for stat in stats]
assert len(all_stats) == 4
def init(context, setup, reset, automate):
"""Walk user through setting up a new config file."""
# print a nice welcome message
click.echo(chanjo.__banner__)
if not automate:
questions = [('sambamba.cov_treshold', 'sufficient coverage',
context.obj.get('sambamba', {}).get('cov_treshold',
[10, 20])),
('database', 'central database path/URI',
context.obj['database'])]
# launch init pipeline
init_pipeline('chanjo', context.obj, questions)
if setup:
chanjo_db = Store(uri=context.obj.user_data['database'])
if reset:
chanjo_db.tear_down()
chanjo_db.set_up()
def init(context, setup, reset, automate, transcripts):
"""Walk user through setting up a new config file."""
# print a nice welcome message
click.echo(chanjo.__banner__)
cov_tresholds = (context.obj.get('sambamba',
{}).get('cov_treshold', [10, 20]))
defaults = {
'sambamba.cov_treshold': {
'value': cov_tresholds,
'prompt': 'sufficient coverage'
},
'database': {
'value': str(context.obj['database']),
'prompt': 'central database path/URI'
}
}
if not automate:
questions = [(key, value['prompt'], value['value'])
for key, value in iteritems(defaults)]
# launch init pipeline
init_pipeline('chanjo', context.obj, questions)
else:
logger.info('setting default config values')
for key, value in iteritems(defaults):
context.obj.set(key, value['value'], scope=context.obj.user_data)
# write to the config file
context.obj.save(default_flow_style=False)
if setup:
only_tx = transcripts or context.obj.get('transcripts') or False
base = TXBASE if only_tx else BASE
chanjo_db = Store(uri=context.obj['database'], base=base)
if reset:
chanjo_db.tear_down()
chanjo_db.set_up()