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)
