gseapy/enrichr.py
def run(self):
        """run enrichr for one sample gene list but multi-libraries"""

        # set organism
        self.get_organism()
        # read input file
        genes_list = self.parse_genelists()
        gss = self.parse_genesets()
        # if gmt
        self._logger.info("Connecting to Enrichr Server to get latest library names")
        if len(gss) < 1:
            sys.stderr.write("Not validated Enrichr library name provided\n")
            sys.stdout.write("Hint: use get_library_name() to view full list of supported names")
            sys.exit(1)
        self.results = pd.DataFrame()

        for g in gss: 
            if isinstance(g, dict): 
                ## local mode
                res = self.enrich(g)
                shortID, self._gs = str(id(g)), "CUSTOM%s"%id(g)
                if res is None: 
                    self._logger.info("No hits return, for gene set: Custom%s"%shortID)
                    continue
            else:
                ## online mode
                self._gs = str(g)
                self._logger.debug("Start Enrichr using library: %s" % (self._gs))
                self._logger.info('Analysis name: %s, Enrichr Library: %s' % (self.descriptions, self._gs))
                shortID, res = self.get_results(genes_list)
                # Remember gene set library used
            res.insert(0, "Gene_set", self._gs)
            # Append to master dataframe
            self.results = self.results.append(res, ignore_index=True, sort=True)
            self.res2d = res
            if self._outdir is None: continue
            self._logger.info('Save file of enrichment results: Job Id:' + str(shortID))
            outfile = "%s/%s.%s.%s.reports.txt" % (self.outdir, self._gs, self.descriptions, self.module)
            self.res2d.to_csv(outfile, index=False, encoding='utf-8', sep="\t")
            # plotting
            if not self.__no_plot:
                msg = barplot(df=res, cutoff=self.cutoff, figsize=self.figsize,
                              top_term=self.__top_term, color='salmon',
                              title=self._gs,
                              ofname=outfile.replace("txt", self.format))
                if msg is not None : self._logger.warning(msg)
            self._logger.info('Done.\n')
        # clean up tmpdir
        if self._outdir is None: self._tmpdir.cleanup()

        return
def run(self):
        # set organism
        self.get_organism()
        # read input file
        genes_list = self.parse_genelists()
        gss = self.parse_genesets()
        # if gmt
        self._logger.info("Connecting to Enrichr Server to get latest library names")
        if len(gss) < 1:
            sys.stderr.write("Not validated Enrichr library name provided\n")
            sys.stdout.write("Hint: use get_library_name() to view full list of supported names")
            sys.exit(1)
        self.results = pd.DataFrame()

        for g in gss: 
            if isinstance(g, dict): 
                ## local mode
                res = self.enrich(g)
                shortID, self._gs = str(id(g)), "CUSTOM%s"%id(g)
                if res is None: 
                    self._logger.info("No hits return, for gene set: Custom%s"%shortID)
                    continue
            else:
                ## online mode
                self._gs = str(g)
                self._logger.debug("Start Enrichr using library: %s" % (self._gs))
                self._logger.info('Analysis name: %s, Enrichr Library: %s' % (self.descriptions, self._gs))
                shortID, res = self.get_results(genes_list)
                # Remember gene set library used
            res.insert(0, "Gene_set", self._gs)
            # Append to master dataframe
            self.results = self.results.append(res, ignore_index=True, sort=True)
            self.res2d = res
            if self._outdir is None: continue
            self._logger.info('Save file of enrichment results: Job Id:' + str(shortID))
            outfile = "%s/%s.%s.%s.reports.txt" % (self.outdir, self._gs, self.descriptions, self.module)
            self.res2d.to_csv(outfile, index=False, encoding='utf-8', sep="\t")
            # plotting
            if not self.__no_plot:
                msg = barplot(df=res, cutoff=self.cutoff, figsize=self.figsize,
                              top_term=self.__top_term, color='salmon',
                              title=self._gs,
                              ofname=outfile.replace("txt", self.format))
                if msg is not None : self._logger.warning(msg)
            self._logger.info('Done.\n')
        # clean up tmpdir
        if self._outdir is None: self._tmpdir.cleanup()

        return
def run ( self ) : # set organism self . get_organism ( ) # read input file genes_list = self . parse_genelists ( ) gss = self . parse_genesets ( ) # if gmt self . _logger . info ( "Connecting to Enrichr Server to get latest library names" ) if len ( gss ) < 1 : sys . stderr . write ( "Not validated Enrichr library name provided\n" ) sys . stdout . write ( "Hint: use get_library_name() to view full list of supported names" ) sys . exit ( 1 ) self . results = pd . DataFrame ( ) for g in gss : if isinstance ( g , dict ) : ## local mode res = self . enrich ( g ) shortID , self . _gs = str ( id ( g ) ) , "CUSTOM%s" % id ( g ) if res is None : self . _logger . info ( "No hits return, for gene set: Custom%s" % shortID ) continue else : ## online mode self . _gs = str ( g ) self . _logger . debug ( "Start Enrichr using library: %s" % ( self . _gs ) ) self . _logger . info ( 'Analysis name: %s, Enrichr Library: %s' % ( self . descriptions , self . _gs ) ) shortID , res = self . get_results ( genes_list ) # Remember gene set library used res . insert ( 0 , "Gene_set" , self . _gs ) # Append to master dataframe self . results = self . results . append ( res , ignore_index = True , sort = True ) self . res2d = res if self . _outdir is None : continue self . _logger . info ( 'Save file of enrichment results: Job Id:' + str ( shortID ) ) outfile = "%s/%s.%s.%s.reports.txt" % ( self . outdir , self . _gs , self . descriptions , self . module ) self . res2d . to_csv ( outfile , index = False , encoding = 'utf-8' , sep = "\t" ) # plotting if not self . __no_plot : msg = barplot ( df = res , cutoff = self . cutoff , figsize = self . figsize , top_term = self . __top_term , color = 'salmon' , title = self . _gs , ofname = outfile . replace ( "txt" , self . format ) ) if msg is not None : self . _logger . warning ( msg ) self . _logger . info ( 'Done.\n' ) # clean up tmpdir if self . _outdir is None : self . _tmpdir . cleanup ( ) return
run enrichr for one sample gene list but multi-libraries
run enrichr for one sample gene list but multi - libraries