def oncodrivefm(project):
log = task.logger
conf = task.conf
log.info("--- [{0}] --------------------------------------------".format(project["id"]))
# configuration
default_filter = get_data_gene_filter_path(conf)
genes_filter_enabled = get_project_conf(conf, project,
"oncodrivefm.genes.filter_enabled", ONCODRIVEFM_GENES_FILTER_ENABLED)
genes_filter = get_project_conf(conf, project, "oncodrivefm.genes.filter", default_filter)
if genes_filter is None: # user can assign a null
genes_filter_enabled = False
genes_filter = default_filter
filt = LabelFilter()
if genes_filter_enabled:
log.info("Loading expression filter ...")
log.debug("> {0}".format(genes_filter))
filt.load(genes_filter)
log.info("Calculating quality indicators for OncodriveFM ...")
qc_data = quality_control(log, conf, project, filt if genes_filter_enabled else None)
project_results = ProjectResults(project)
project_results.save_quality_control("oncodrivefm", qc_data)
def load_expression_filter(log, conf, project):
default_filter = get_data_gene_filter_path(conf)
genes_filter_enabled = get_project_conf(conf, project,
"oncodrivefm.genes.filter_enabled", ONCODRIVEFM_GENES_FILTER_ENABLED)
genes_filter = get_project_conf(conf, project, "oncodrivefm.genes.filter", default_filter)
if genes_filter is None: # user can assign a null
genes_filter_enabled = False
genes_filter = default_filter
filt = LabelFilter()
if genes_filter_enabled:
log.info("Loading expression filter ...")
log.debug("> {0}".format(genes_filter))
filt.load(genes_filter)
return genes_filter_enabled, genes_filter, filt
def get_oncodrivefm_configuration(log, conf, project, num_samples):
log.info("OncodriveFM configuration:")
num_cores = get_project_conf(conf, project, "oncodrivefm.num_cores", ONCODRIVEFM_NUM_CORES)
estimator = get_project_conf(conf, project, "oncodrivefm.estimator", ONCODRIVEFM_ESTIMATOR)
log.info(" num_cores = {0}".format(num_cores))
log.info(" estimator = {0}".format(estimator))
log.info(" Genes:")
genes_num_samplings = get_project_conf(conf, project,
"oncodrivefm.genes.num_samplings", ONCODRIVEFM_GENES_NUM_SAMPLINGS)
genes_threshold = get_threshold(log, conf, project,
"oncodrivefm.genes.threshold", ONCODRIVEFM_GENES_THRESHOLD, num_samples)
genes_filter_enabled, genes_filter, filt = load_expression_filter(log, conf, project)
log.info(" num_samplings = {0}".format(genes_num_samplings))
log.info(" threshold = {0}".format(genes_threshold))
log.info(" filter enabled = {0}".format(genes_filter_enabled))
log.info(" filter = {0}".format(os.path.basename(genes_filter) if genes_filter is not None else None))
log.info(" Pathways:")
pathways_num_samplings = get_project_conf(conf, project,
"oncodrivefm.pathways.num_samplings", ONCODRIVEFM_PATHWAYS_NUM_SAMPLINGS)
pathways_threshold = get_threshold(log, conf, project,
"oncodrivefm.pathways.threshold", ONCODRIVEFM_PATHWAYS_THRESHOLD, num_samples)
log.info(" num_samplings = {0}".format(pathways_num_samplings))
log.info(" threshold = {0}".format(pathways_threshold))
return (num_cores, estimator,
genes_num_samplings, genes_threshold, genes_filter_enabled, genes_filter, filt,
pathways_num_samplings, pathways_threshold)
def get_threshold(log, conf, project, key, default, num_samples):
threshold = get_project_conf(conf, project, key, default)
try:
threshold = int(threshold)
except:
if isinstance(threshold, basestring) and threshold.endswith("%"):
try:
threshold = max(num_samples * int(threshold[0:-1]) / 100, 2)
except:
log.warn("Wrong threshold value for '{0}'. Using the default value '{1}' instead.".format(threshold[0:-1], default))
threshold = default
else:
log.warn("Wrong threshold value for '{0}'. Using the default value '{1}' instead.".format(threshold, default))
threshold = default
return threshold
def get_oncodriveclust_configuration(log, conf, project):
log.info("OncodriveCLUST configuration:")
mutations_threshold = get_project_conf(conf, project, "oncodriveclust.mutations_threshold", ONCODRIVECLUST_MUTATIONS_THRESHOLD)
default_filter = get_data_gene_filter_path(conf)
genes_filter_enabled = get_project_conf(conf, project, "oncodriveclust.genes_filter_enabled", ONCODRIVECLUST_GENES_FILTER_ENABLED)
genes_filter = get_project_conf(conf, project, "oncodriveclust.genes_filter", default_filter)
if genes_filter is None: # user can assign a null
genes_filter_enabled = False
genes_filter = default_filter
log.info(" mutations_threshold = {0}".format(mutations_threshold))
log.info(" genes_filter_enabled = {0}".format(genes_filter_enabled))
log.info(" genes_filter = {0}".format(os.path.basename(genes_filter)))
filt = LabelFilter()
if genes_filter_enabled:
log.info("Loading expression filter ...")
log.debug("> {0}".format(genes_filter))
filt.load(genes_filter)
return (mutations_threshold, genes_filter_enabled, genes_filter, filt)
