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_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)