parser.add_option("-p","--parameters",action="store",dest="parameters",help="FILE with additional, classifier-specific parameters. (confounders for CWMI)",metavar="FILE",default=None)
parser.add_option("-x","--profile",action="store_true",dest="profile",help="Profile the code",default=False)
# RVF add option save crossval files
parser.add_option("-y","--save_crossval_files",action="store_true",dest="crossval_files",help="Save the training and test sets for crossvalidation to files under /crossvalidation",default=False)
parser.add_option("-d","--metadata",help="Load metadata from FILE and add to misclassification report [default: %default]",metavar="FILE",default=None)
parser.add_option("-f","--feature_select",help="Model file (currently only association rule files) with features to select from [default: %default]",metavar="FILE",default=None)
parser.add_option("-1","--feature_select_score",help="Order features by (feature selection option)", default="order_cwmi")
parser.add_option("-n","--feature_select_top_n",help="Take the top n features(feature selection option)", type="int", default=20)
(options, args) = parser.parse_args()
# Check arguments for crucial errors
errorCount = 0
if not options.input_samples_filename:
error("Please provide a genotype sample file with -s /path/to/genotype.file")
errorCount += 1
if not options.input_classes_filename:
error("Please provide a phenotype class file with -c /path/to/phenotype.file")
errorCount += 1
if not options.target_class:
error("Please provide the phenotype target to be predicted with -t \"TRAITNAME\"")
errorCount += 1
if not options.output_filename:
error("Please specify a file for the output with -o /path/to/result.file")
errorCount += 1
if errorCount > 0:
error("For help on usage, try calling:\n\tpython %s -h" % os.path.basename(sys.argv[0]))
exit(1)
fileio = FileIO()
parser.add_option("-k","--svm_cost",action="store",dest="C",metavar="FLOAT",help="Set the SVM misclassification penalty parameter C to FLOAT")
parser.add_option("-s","--samples",action="store",dest="input_samples_filename",help="Read samples from FILE",metavar="FILE")
parser.add_option("-c","--classes",action="store",dest="input_classes_filename",help="Read class labels from FILE",metavar="FILE")
parser.add_option("-t","--targetclass",action="store",dest="target_class",help="Set the target CLASS for testing",metavar="CLASS")
parser.add_option("-o","--output",action="store",dest="output_filename",help="Write rules to FILE",metavar="FILE",default=None)
parser.add_option("-p","--parameters",action="store",dest="parameters",help="FILE with additional, classifier-specific parameters. (confounders for CWMI)",metavar="FILE",default="taxonomic_confounders.txt")
parser.add_option("-f","--feature_select",help="Model file (currently only association rule files) with features to select from [default: %default]",metavar="FILE",default=None)
parser.add_option("-1","--feature_select_score",help="Order features by (feature selection option)", default="order_cwmi")
parser.add_option("-n","--feature_select_top_n",help="Take the top n features(feature selection option)", type="int", default=20)
(options, args) = parser.parse_args()
# Check arguments for crucial errors
errorCount = 0
if not options.input_samples_filename:
error("Please provide a genotype sample file with -s /path/to/genotype.file")
errorCount += 1
if not options.input_classes_filename:
error("Please provide a phenotype class file with -c /path/to/phenotype.file")
errorCount += 1
if not options.target_class:
error("Please provide the phenotype target to be predicted with -t \"TRAITNAME\"")
errorCount += 1
if errorCount > 0:
error("For help on usage, try calling:\n\tpython %s -h" % os.path.basename(sys.argv[0]))
exit(1)
pt.start()
fileio = FileIO()
samples = fileio.load_samples(options.input_samples_filename)
samples_time = pt.stop()
default="libsvm.libSVMClassifier")
parser.add_option(
"-p",
"--parameters",
action="store",
dest="parameters",
help="FILE with additional, classifier-specific parameters.",
metavar="FILE",
default=None)
(options, args) = parser.parse_args()
# Check arguments for crucial errors
errorCount = 0
if not options.input_samples_filename:
error(
"Please provide a genotype sample file with -s /path/to/genotype.file"
)
errorCount += 1
if not options.model_filename:
error(
"Please provide a model file for this phenotype with -m /path/to/model.file"
)
errorCount += 1
if not options.target_class:
error(
"Please provide the phenotype target to be predicted with -t \"TRAITNAME\""
)
errorCount += 1
if errorCount > 0:
error("For help on usage, try calling:\n\tpython %s -h" %
os.path.basename(sys.argv[0]))