def _annotateTest(self, inputFilename, outputFilename, datasource_dir, inputFormat="MAFLITE", outputFormat="TCGAMAF", default_annotations=TCGA_MAF_DEFAULTS, override_annotations=None, is_skip_no_alts=False):
self.logger.info("Initializing Annotator...")
if override_annotations is None:
override_annotations = dict()
annotator = Annotator()
runSpec = OncotatorCLIUtils.create_run_spec(inputFormat, outputFormat, inputFilename, outputFilename, defaultAnnotations=default_annotations, datasourceDir=datasource_dir, globalAnnotations=override_annotations, is_skip_no_alts=is_skip_no_alts)
annotator.initialize(runSpec)
self.logger.info("Annotation starting...")
return annotator.annotate()
def main(argv=None): # IGNORE:C0111
"""Command line options."""
from oncotator.utils.OncotatorCLIUtils import OncotatorCLIUtils
from oncotator.Annotator import Annotator
if argv is None:
argv = sys.argv
else:
sys.argv.extend(argv)
program_version = "%s" % __version__
program_build_date = str(__updated__)
program_version_message = '%%(prog)s %s' % (program_version)
program_shortdesc = program_version_message
program_license = '''%s
%s
Copyright 2012 Broad Institute. All rights reserved.
#TODO: License Here
Distributed on an "AS IS" basis without warranties
or conditions of any kind, either express or implied.
USAGE
''' % (program_shortdesc, str(__date__))
try:
args = parseOptions(program_license, program_version_message)
verbose = args.verbose
if verbose > 0:
print("Verbose mode on")
logFilename = args.log_name # 'oncotator.log'
# Create a basic logger to a file
loggingFormat = '%(asctime)s %(levelname)s [%(name)s:%(lineno)d] %(message)s'
logging.basicConfig(filename=logFilename, level=logging.INFO, format=loggingFormat)
# Add a console logger to the root logger, which means that all loggers generated will have the console dump.
# Output on the console will be the same as what is in the log file.
ch = logging.StreamHandler()
ch.setLevel(logging.WARN)
formatter = logging.Formatter(loggingFormat)
ch.setFormatter(formatter)
if verbose:
ch.setLevel(logging.INFO)
print("Path:")
print(sys.path)
print(" ")
logging.getLogger('').addHandler(ch)
logger = logging.getLogger(__name__)
logger.info("Oncotator " + program_version)
logger.info("Args: " + str(args))
logger.info('Log file: ' + os.path.abspath(logFilename))
if DEBUG:
logger.setLevel(logging.DEBUG)
# Initiate an Oncotator session.
inputFilename = os.path.expanduser(args.input_file)
outputFilename = os.path.expanduser(args.output_file)
inputFormat = args.input_format.upper()
outputFormat = args.output_format.upper()
datasourceDir = os.path.expanduser(args.dbDir)
cache_url = args.cache_url
read_only_cache = args.read_only_cache
tx_mode = args.tx_mode
is_skip_no_alts = args.skip_no_alt
genome_build = args.genome_build
is_no_prepend = not args.prepend
# Parse annotation overrides
commandLineManualOverrides = args.override_cli
overrideConfigFile = args.override_config
if overrideConfigFile is not None and not os.path.exists(overrideConfigFile):
logger.warn("Could not find " + overrideConfigFile + " ... proceeding anyway.")
overrideConfigFile = None
manualOverrides = OncotatorCLIUtils.determineAllAnnotationValues(commandLineManualOverrides, overrideConfigFile)
# Parse default overrides
commandLineDefaultValues = args.default_cli
defaultConfigFile = args.default_config
if defaultConfigFile is not None and not os.path.exists(defaultConfigFile):
if defaultConfigFile != DEFAULT_DEFAULT_ANNOTATIONS:
logger.warn("Could not find " + defaultConfigFile + " ... proceeding anyway.")
else:
logger.info("Could not find Broad-specific " + defaultConfigFile + " ... proceeding without any default annotations. __UNKNOWN__ may appear in TCGA MAF outputs.")
defaultConfigFile = None
defaultValues = OncotatorCLIUtils.determineAllAnnotationValues(commandLineDefaultValues, defaultConfigFile)
if is_skip_no_alts and (outputFormat == "VCF"):
logging.getLogger(__name__).warn("--skip-no-alt specified when output is a VCF. This is likely to generate errors.")
if is_skip_no_alts and (inputFormat != "VCF"):
logging.getLogger(__name__).info("--skip-no-alt specified when input is not VCF. skip-no-alt is not going to do anything.")
if is_no_prepend and (outputFormat != "TCGAMAF"):
logging.getLogger(__name__).info("no prepend specified when output is not TCGAMAF. Ignoring and proceeding.")
if outputFormat=="TCGAVCF":
logging.getLogger(__name__).warning("TCGA VCF output is not supported and should be considered experimental when used outside of the Broad Institute. Outside of the Broad Institute, use of -o VCF is more likely to be desired by users.")
# Create a run configuration to pass to the Annotator class.
runConfig = OncotatorCLIUtils.create_run_spec(inputFormat, outputFormat, inputFilename, outputFilename,
globalAnnotations=manualOverrides, datasourceDir=datasourceDir,
isMulticore=(not args.noMulticore),
defaultAnnotations=defaultValues, cacheUrl=cache_url,
read_only_cache=read_only_cache, tx_mode=tx_mode,
is_skip_no_alts=is_skip_no_alts, genomeBuild=genome_build,
other_opts=determineOtherOptions(args, logger))
annotator = Annotator()
annotator.initialize(runConfig)
annotator.annotate()
return 0
except KeyboardInterrupt:
### handle keyboard interrupt ###
return 0
