gseapy/gsea.py
def _download_libraries(self, libname):
        """ download enrichr libraries."""
        self._logger.info("Downloading and generating Enrichr library gene sets......")
        s = retry(5)
        # queery string
        ENRICHR_URL = 'http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary'
        query_string = '?mode=text&libraryName=%s'
        # get
        response = s.get( ENRICHR_URL + query_string % libname, timeout=None)
        if not response.ok:
            raise Exception('Error fetching enrichment results, check internet connection first.')
        # reformat to dict and save to disk
        mkdirs(DEFAULT_CACHE_PATH)
        genesets_dict = {}
        outname = "enrichr.%s.gmt"%libname
        gmtout = open(os.path.join(DEFAULT_CACHE_PATH, outname), "w")
        for line in response.iter_lines(chunk_size=1024, decode_unicode='utf-8'):
            line=line.strip()
            k = line.split("\t")[0]
            v = list(map(lambda x: x.split(",")[0], line.split("\t")[2:]))
            genesets_dict.update({ k: v})
            outline = "%s\t\t%s\n"%(k, "\t".join(v))
            gmtout.write(outline)
        gmtout.close()

        return genesets_dict
def _download_libraries(self, libname):
        self._logger.info("Downloading and generating Enrichr library gene sets......")
        s = retry(5)
        # queery string
        ENRICHR_URL = 'http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary'
        query_string = '?mode=text&libraryName=%s'
        # get
        response = s.get( ENRICHR_URL + query_string % libname, timeout=None)
        if not response.ok:
            raise Exception('Error fetching enrichment results, check internet connection first.')
        # reformat to dict and save to disk
        mkdirs(DEFAULT_CACHE_PATH)
        genesets_dict = {}
        outname = "enrichr.%s.gmt"%libname
        gmtout = open(os.path.join(DEFAULT_CACHE_PATH, outname), "w")
        for line in response.iter_lines(chunk_size=1024, decode_unicode='utf-8'):
            line=line.strip()
            k = line.split("\t")[0]
            v = list(map(lambda x: x.split(",")[0], line.split("\t")[2:]))
            genesets_dict.update({ k: v})
            outline = "%s\t\t%s\n"%(k, "\t".join(v))
            gmtout.write(outline)
        gmtout.close()

        return genesets_dict
def _download_libraries ( self , libname ) : self . _logger . info ( "Downloading and generating Enrichr library gene sets......" ) s = retry ( 5 ) # queery string ENRICHR_URL = 'http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary' query_string = '?mode=text&libraryName=%s' # get response = s . get ( ENRICHR_URL + query_string % libname , timeout = None ) if not response . ok : raise Exception ( 'Error fetching enrichment results, check internet connection first.' ) # reformat to dict and save to disk mkdirs ( DEFAULT_CACHE_PATH ) genesets_dict = { } outname = "enrichr.%s.gmt" % libname gmtout = open ( os . path . join ( DEFAULT_CACHE_PATH , outname ) , "w" ) for line in response . iter_lines ( chunk_size = 1024 , decode_unicode = 'utf-8' ) : line = line . strip ( ) k = line . split ( "\t" ) [ 0 ] v = list ( map ( lambda x : x . split ( "," ) [ 0 ] , line . split ( "\t" ) [ 2 : ] ) ) genesets_dict . update ( { k : v } ) outline = "%s\t\t%s\n" % ( k , "\t" . join ( v ) ) gmtout . write ( outline ) gmtout . close ( ) return genesets_dict
download enrichr libraries.
download enrichr libraries .