def gsea_edb_parser(results_path, index=0):
    """Parse results.edb file stored under **edb** file folder.

    :param results_path: the .results file located inside edb folder.
    :param index: gene_set index of gmt database, used for iterating items.
    :return: enrichment_term, hit_index,nes, pval, fdr.
    """
    from bs4 import BeautifulSoup

    soup = BeautifulSoup(open(results_path), features='xml')
    tag = soup.findAll('DTG')
    term = dict(tag[index].attrs)
    # dict_keys(['RANKED_LIST', 'GENESET', 'FWER', 'ES_PROFILE',
    # 'HIT_INDICES', 'ES', 'NES', 'TEMPLATE', 'RND_ES', 'RANK_SCORE_AT_ES',
    # 'NP', 'RANK_AT_ES', 'FDR'])
    enrich_term = term.get('GENESET').split("#")[1]
    es_profile = term.get('ES_PROFILE').split(" ")
    # rank_es = term.get('RND_ES').split(" ")
    hit_ind =term.get('HIT_INDICES').split(" ")
    es_profile = [float(i) for i in es_profile ]
    hit_ind = [float(i) for i in hit_ind ]
    #r ank_es = [float(i) for i in rank_es ]
    nes = term.get('NES')
    pval = term.get('NP')
    fdr =  term.get('FDR')
    # fwer = term.get('FWER')
    # index_range = len(tag)-1
    logging.debug("Enriched Gene set is: "+ enrich_term)

    return enrich_term, hit_ind, nes, pval, fdr
def gsea_edb_parser(results_path, index=0):
    """Parse results.edb file stored under **edb** file folder.

    :param results_path: the .results file located inside edb folder.
    :param index: gene_set index of gmt database, used for iterating items.
    :return: enrichment_term, hit_index,nes, pval, fdr.
    """
    from bs4 import BeautifulSoup

    soup = BeautifulSoup(open(results_path), features='xml')
    tag = soup.findAll('DTG')
    term = dict(tag[index].attrs)
    # dict_keys(['RANKED_LIST', 'GENESET', 'FWER', 'ES_PROFILE',
    # 'HIT_INDICES', 'ES', 'NES', 'TEMPLATE', 'RND_ES', 'RANK_SCORE_AT_ES',
    # 'NP', 'RANK_AT_ES', 'FDR'])
    enrich_term = term.get('GENESET').split("#")[1]
    es_profile = term.get('ES_PROFILE').split(" ")
    # rank_es = term.get('RND_ES').split(" ")
    hit_ind =term.get('HIT_INDICES').split(" ")
    es_profile = [float(i) for i in es_profile ]
    hit_ind = [float(i) for i in hit_ind ]
    #r ank_es = [float(i) for i in rank_es ]
    nes = term.get('NES')
    pval = term.get('NP')
    fdr =  term.get('FDR')
    # fwer = term.get('FWER')
    # index_range = len(tag)-1
    logging.debug("Enriched Gene set is: "+ enrich_term)

    return enrich_term, hit_ind, nes, pval, fdr
def gsea_edb_parser ( results_path , index = 0 ) : from bs4 import BeautifulSoup soup = BeautifulSoup ( open ( results_path ) , features = 'xml' ) tag = soup . findAll ( 'DTG' ) term = dict ( tag [ index ] . attrs ) # dict_keys(['RANKED_LIST', 'GENESET', 'FWER', 'ES_PROFILE', # 'HIT_INDICES', 'ES', 'NES', 'TEMPLATE', 'RND_ES', 'RANK_SCORE_AT_ES', # 'NP', 'RANK_AT_ES', 'FDR']) enrich_term = term . get ( 'GENESET' ) . split ( "#" ) [ 1 ] es_profile = term . get ( 'ES_PROFILE' ) . split ( " " ) # rank_es = term.get('RND_ES').split(" ") hit_ind = term . get ( 'HIT_INDICES' ) . split ( " " ) es_profile = [ float ( i ) for i in es_profile ] hit_ind = [ float ( i ) for i in hit_ind ] #r ank_es = [float(i) for i in rank_es ] nes = term . get ( 'NES' ) pval = term . get ( 'NP' ) fdr = term . get ( 'FDR' ) # fwer = term.get('FWER') # index_range = len(tag)-1 logging . debug ( "Enriched Gene set is: " + enrich_term ) return enrich_term , hit_ind , nes , pval , fdr
Parse results.edb file stored under **edb** file folder.

    :param results_path: the .results file located inside edb folder.
    :param index: gene_set index of gmt database, used for iterating items.
    :return: enrichment_term, hit_index,nes, pval, fdr.
Parse results . edb file stored under ** edb ** file folder .