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self.max_size=max_size
self.permutation_num=int(permutation_num) if int(permutation_num) > 0 else 0
self.weighted_score_type=weighted_score_type
self.ascending=ascending
self._processes=processes
self.figsize=figsize
self.format=format
self.graph_num=int(graph_num)
self.seed=seed
self.verbose=bool(verbose)
self.module='gsea'
self.ranking=None
self._noplot=no_plot
# init logger
logfile = self.prepare_outdir()
self._logger = log_init(outlog=logfile,
log_level=logging.INFO if self.verbose else logging.WARNING)
self.indir=indir
self.outdir=outdir
self.weighted_score_type=weighted_score_type
self.min_size=min_size
self.max_size=max_size
self.figsize=figsize
self.fignum=int(graph_num)
self.format=format
self.verbose=bool(verbose)
self.module='replot'
self.gene_sets=None
self.ascending=False
# init logger
mkdirs(self.outdir)
outlog = os.path.join(self.outdir,"gseapy.%s.%s.log"%(self.module,"run"))
self._logger = log_init(outlog=outlog,
log_level=logging.INFO if self.verbose else logging.WARNING)
def run(self):
self.max_size=max_size
self.permutation_num=int(permutation_num) if int(permutation_num) > 0 else 0
self.ascending=ascending
self.figsize=figsize
self.format=format
self.graph_num=int(graph_num)
self.seed=seed
self.verbose=bool(verbose)
self.ranking=None
self.module='ssgsea'
self._processes=processes
self._noplot=no_plot
# init logger
logfile = self.prepare_outdir()
self._logger = log_init(outlog=logfile,
log_level=logging.INFO if self.verbose else logging.WARNING)