def __init__(self, function_id, cmrun, seqtype):
"""creates a ScoringFunction"""
scoring.ScoringFunctionBase.__init__(self, function_id, cmrun)
# attributes accessible by subclasses
self.seqtype = seqtype
self.__setup_meme_suite(cmrun.config_params)
self.num_motif_func = util.get_iter_fun(
cmrun.config_params['MEME'], "nmotifs",
cmrun.config_params['num_iterations'])
self.__last_motif_infos = None
self.__last_iteration_result = {}
self.all_pvalues = None
self.last_result = None
self.update_log = scoring.RunLog(("%s-score-" % function_id) + seqtype,
cmrun.dbsession(),
cmrun.config_params)
self.motif_log = scoring.RunLog(("%s-motif-" % function_id) + seqtype,
cmrun.dbsession(), cmrun.config_params)
used_genes = sorted(cmrun.ratios.row_names)
self.used_seqs = cmrun.organism().sequences_for_genes_scan(
used_genes, seqtype=self.seqtype)
logging.debug("building reverse map...")
start_time = util.current_millis()
self.reverse_map = self.__build_reverse_map(cmrun.ratios)
logging.debug("reverse map built in %d ms.",
util.current_millis() - start_time)
self.__last_results = None # caches the results of the previous meme run
def __init__(self, organism, membership, ratios, config_params=None):
"""Create scoring function instance"""
scoring.ScoringFunctionBase.__init__(self, "SetEnrichment", organism,
membership, ratios, config_params)
self.__set_types = read_set_types(config_params, organism.thesaurus(),
ratios.row_names)
self.run_log = scoring.RunLog('set_enrichment', config_params)
def __init__(self, function_id, cmrun):
"""Create scoring function instance"""
scoring.ScoringFunctionBase.__init__(self, function_id, cmrun)
self.__set_types = read_set_types(self.config_params,
self.organism.thesaurus(),
self.ratios.row_names)
self.run_log = scoring.RunLog(function_id, cmrun.dbsession(),
self.config_params)
def __init__(self, organism, membership, ratios, config_params):
"""Create scoring function instance"""
scoring.ScoringFunctionBase.__init__(self, "Rows", organism,
membership, ratios, config_params)
self.run_log = scoring.RunLog("row_scoring", config_params)
def __init__(self, organism, membership, ratios, config_params):
"""Create scoring function instance"""
scoring.ScoringFunctionBase.__init__(self, "Networks", organism, membership,
ratios, config_params)
self.__networks = None
self.run_log = scoring.RunLog("network", config_params)
def __init__(self, function_id, cmrun):
"""Create scoring function instance"""
scoring.ScoringFunctionBase.__init__(self, function_id, cmrun)
self.run_log = scoring.RunLog(function_id, cmrun.dbsession(),
cmrun.config_params)