def __init__(self, id, organism, membership, ratios, seqtype, config_params=None):
"""creates a ScoringFunction"""
scoring.ScoringFunctionBase.__init__(self, id, organism, membership,
ratios, config_params=config_params)
# attributes accessible by subclasses
self.seqtype = seqtype
self.__setup_meme_suite(config_params)
self.num_motif_func = util.get_iter_fun(config_params['MEME'], "nmotifs",
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("motif-score-" + seqtype, config_params)
self.motif_log = scoring.RunLog("motif-motif-" + seqtype, config_params)
used_genes = sorted(ratios.row_names)
self.used_seqs = 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(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, 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 get_scaling(params, id):
"""returns a scaling function for the given prefix from the configuration parameters"""
scaling = params[id]
return util.get_iter_fun(params, prefix + "scaling", params["num_iterations"])
def get_scaling(params, id):
"""returns a scaling function for the given prefix from the configuration parameters"""
scaling = params[id]
return util.get_iter_fun(params, prefix + 'scaling',
params['num_iterations'])
