def main_cmd():
"""
Entry point for command line.
"""
# build description string based on available methods
desc_string = "Command-line driver for Enrich2 v{}".format(__version__) + \
"\n\nscoring methods:\n" + \
"\n".join([" {:22}{}".format(k, v) for k, v in
list(SCORING_METHODS.items())]) + \
"\n\nlog ratio methods:\n" + \
"\n".join([" {:22}{}".format(k, v) for k, v in
list(LOGR_METHODS.items())])
# create parser and add description
parser = ArgumentParser(prog="Enrich2",
description=desc_string,
formatter_class=RawDescriptionHelpFormatter)
# add command line arguments
parser.add_argument("config", help="JSON configuration file")
parser.add_argument("scoring_method",
help="scoring method",
choices=list(SCORING_METHODS.keys()))
parser.add_argument("logr_method",
help="log ratio method",
choices=list(LOGR_METHODS.keys()))
# add support for semantic version checking
parser.add_argument("--version",
action="version",
version="%(prog)s {}".format(__version__))
# add analysis options
parser.add_argument("--log",
metavar="FILE",
dest="log_file",
help="path to log file")
parser.add_argument("--no-plots",
dest="plots_requested",
action="store_false",
default=True,
help="don't make plots")
parser.add_argument("--no-tsv",
dest="tsv_requested",
action="store_false",
default=True,
help="don't generate tsv files")
parser.add_argument("--recalculate",
dest="force_recalculate",
action="store_true",
default=False,
help="force recalculation")
parser.add_argument("--component-outliers",
dest="component_outliers",
action="store_true",
default=False,
help="calculate component outlier stats")
parser.add_argument("--output-dir",
metavar="DIR",
dest="output_dir_override",
help="override the config file's output directory")
parser.add_argument("--sfmap-aa-file",
metavar="FILE",
dest="sfmap_aa_file",
help="amino acid groups for sequence-function maps")
args = parser.parse_args()
# start the logs
start_logging(args.log_file, logging.DEBUG)
# read the JSON file
try:
cfg = json.load(open(args.config, "U"))
except IOError:
raise IOError("Failed to open '{}' [{}]".format(
args.config, DRIVER_NAME))
except ValueError:
raise ValueError(
"Improperly formatted .json file [{}]".format(DRIVER_NAME))
# identify config file type and create the object
if config_check.is_experiment(cfg):
logging.info("Detected an Experiment config file",
extra={'oname': DRIVER_NAME})
obj = Experiment()
elif config_check.is_selection(cfg):
logging.info("Detected a Selection config file",
extra={'oname': DRIVER_NAME})
obj = Selection()
elif config_check.is_seqlib(cfg):
seqlib_type = config_check.seqlib_type(cfg)
logging.info("Detected a %s config file",
seqlib_type,
extra={'oname': DRIVER_NAME})
if seqlib_type == "BarcodeSeqLib":
obj = BarcodeSeqLib()
elif seqlib_type == "BcidSeqLib":
obj = BcidSeqLib()
elif seqlib_type == "BcvSeqLib":
obj = BcvSeqLib()
elif seqlib_type == "BasicSeqLib":
obj = BasicSeqLib()
elif seqlib_type == "OverlapSeqLib":
obj = OverlapSeqLib()
elif seqlib_type == "IdOnlySeqLib":
obj = IdOnlySeqLib()
else:
raise ValueError("Unrecognized SeqLib type '{}' [{}]".format(
seqlib_type, DRIVER_NAME))
else:
raise ValueError("Unrecognized .json config [{}]".format(DRIVER_NAME))
# set analysis options
obj.force_recalculate = args.force_recalculate
obj.component_outliers = args.component_outliers
obj.scoring_method = args.scoring_method
obj.logr_method = args.logr_method
obj.plots_requested = args.plots_requested
obj.tsv_requested = args.tsv_requested
if args.output_dir_override is not None:
obj.output_dir_override = True
obj.output_dir = args.output_dir_override
else:
obj.output_dir_override = False
if args.sfmap_aa_file is not None:
obj.plot_options = dict()
obj.plot_options['aa_list'], obj.plot_options['aa_label_groups'] = \
parse_aa_list(args.sfmap_aa_file)
# configure the object
obj.configure(cfg)
# make sure objects are valid
try:
obj.validate()
except ValueError:
logging.exception("Invalid configuration",
extra={'oname': DRIVER_NAME})
else:
# open HDF5 files for the object and all child objects
obj.store_open(children=True)
# perform the analysis
obj.calculate()
# generate desired output
obj.make_plots()
try:
obj.make_plots()
except Exception:
logging.exception("Calculations completed, but plotting failed.",
extra={'oname': DRIVER_NAME})
try:
obj.write_tsv()
except Exception:
logging.exception("Calculations completed, but TSV ouput failed.",
extra={'oname': DRIVER_NAME})
# clean up
obj.store_close(children=True)
def main_cmd():
"""
Entry point for command line.
"""
# build description string based on available methods
desc_string = "Command-line driver for Enrich2." + \
"\n\nscoring methods:\n" + \
"\n".join([" {:22}{}".format(k, v) for k, v in available_scoring_methods.items()]) + \
"\n\nlog ratio methods:\n" + \
"\n".join([" {:22}{}".format(k, v) for k, v in available_logr_methods.items()])
# create parser and add description
parser = argparse.ArgumentParser(
description=desc_string,
formatter_class=argparse.RawDescriptionHelpFormatter)
# add command line arguments
parser.add_argument("config", help="JSON configuration file")
parser.add_argument("scoring_method",
help="scoring method",
choices=available_scoring_methods.keys())
parser.add_argument("logr_method",
help="log ratio method",
choices=available_logr_methods.keys())
# add analysis options
parser.add_argument("--log",
dest="log_file",
metavar="FILE",
help="path to log file")
parser.add_argument("--no-plots",
help="don't make plots",
dest="plots_requested",
action="store_false",
default=True)
parser.add_argument("--no-tsv",
help="don't generate tsv files",
dest="tsv_requested",
action="store_false",
default=True)
parser.add_argument("--recalculate",
help="force recalculation",
dest="force_recalculate",
action="store_true",
default=False)
parser.add_argument("--component-outliers",
help="calculate component outlier stats",
dest="component_outliers",
action="store_true",
default=False)
parser.add_argument("--output-dir",
help="override the config file's output directory",
dest="output_dir_override",
metavar="DIR")
args = parser.parse_args()
# start the logs
start_logging(args.log_file, logging.DEBUG)
# read the JSON file
try:
cfg = json.load(open(args.config, "U"))
except IOError:
raise IOError("Failed to open '{}' [{}]".format(
args.config, driver_name))
except ValueError:
raise ValueError(
"Improperly formatted .json file [{}]".format(driver_name))
# identify config file type and create the object
if config_check.is_experiment(cfg):
logging.info("Detected an Experiment config file",
extra={'oname': driver_name})
obj = Experiment()
elif config_check.is_selection(cfg):
logging.info("Detected a Selection config file",
extra={'oname': driver_name})
obj = Selection()
elif config_check.is_seqlib(cfg):
seqlib_type = config_check.seqlib_type(cfg)
logging.info("Detected a {} config file".format(seqlib_type),
extra={'oname': driver_name})
obj = globals()[seqlib_type]()
else:
raise ValueError("Unrecognized .json config [{}]".format(driver_name))
# set analysis options
obj.force_recalculate = args.force_recalculate
obj.component_outliers = args.component_outliers
obj.scoring_method = args.scoring_method
obj.logr_method = args.logr_method
obj.plots_requested = args.plots_requested
obj.tsv_requested = args.tsv_requested
if args.output_dir_override is not None:
obj.output_dir_override = True
obj.output_dir = args.output_dir_override
else:
obj.output_dir_override = False
# configure the object
obj.configure(cfg)
# make sure objects are valid
try:
obj.validate()
except ValueError, e:
logging.error("Invalid settings: {}".format(e),
extra={'oname': driver_name})