gseapy/gsea.py
def run(self):
        """run entry"""
        self._logger.info("Parsing data files for ssGSEA...........................")
        # load data
        data = self.load_data()
        # normalized samples, and rank
        normdat = self.norm_samples(data)
        # filtering out gene sets and build gene sets dictionary
        gmt = self.load_gmt(gene_list=normdat.index.values, gmt=self.gene_sets)
        self._logger.info("%04d gene_sets used for further statistical testing....."% len(gmt))
        # set cpu numbers
        self._set_cores()
        # start analsis
        self._logger.info("Start to run ssGSEA...Might take a while................")
        if self.permutation_num == 0 :
            # ssGSEA without permutation
            self.runSamples(df=normdat, gmt=gmt)
        else:
            # run permutation procedure and calculate pvals, fdrs
            self._logger.warning("run ssGSEA with permutation procedure, don't use these part of results for publication.")
            self.runSamplesPermu(df=normdat, gmt=gmt)
        # clean up all outputs if _outdir is None
        if self._outdir is None:
            self._tmpdir.cleanup()
def run(self):
        """run entry"""
        self._logger.info("Parsing data files for ssGSEA...........................")
        # load data
        data = self.load_data()
        # normalized samples, and rank
        normdat = self.norm_samples(data)
        # filtering out gene sets and build gene sets dictionary
        gmt = self.load_gmt(gene_list=normdat.index.values, gmt=self.gene_sets)
        self._logger.info("%04d gene_sets used for further statistical testing....."% len(gmt))
        # set cpu numbers
        self._set_cores()
        # start analsis
        self._logger.info("Start to run ssGSEA...Might take a while................")
        if self.permutation_num == 0 :
            # ssGSEA without permutation
            self.runSamples(df=normdat, gmt=gmt)
        else:
            # run permutation procedure and calculate pvals, fdrs
            self._logger.warning("run ssGSEA with permutation procedure, don't use these part of results for publication.")
            self.runSamplesPermu(df=normdat, gmt=gmt)
        # clean up all outputs if _outdir is None
        if self._outdir is None:
            self._tmpdir.cleanup()
run entry