def model_from_bam(args):
"""Main function for the `iss model` submodule
This submodule write all variables necessary for building an ErrorModel
to args.output + .npz
Args:
args (object): the command-line arguments from argparse
"""
logger = logging.getLogger(__name__)
logger.debug('iss version %s' % __version__)
logger.debug('Using verbose logger')
try: # try to import bam module and write model data to file
logger.info('Starting iss model')
from iss import bam
except ImportError as e:
logger.error('Failed to import bam module: %s' % e)
sys.exit(1)
else:
logger.info('Using KDE ErrorModel')
bam.to_model(args.bam, args.output)
logger.info('Model generation complete')
def test_to_model():
bam_file = 'data/ecoli.bam'
output = 'data/test_bam'
bam.to_model(bam_file, output)
os.remove(output + '.npz')