import cPickle import sp_tools #load up the pre-pickled data papersExp_handle = open('Uniprot-Bias/goa_exp_papers.pik', 'rb') papersExp_dict = cPickle.load(papersExp_handle) papers_protsExp_handle = open('Uniprot-Bias/goa_exp_papers_prots.pik', 'rb') papers_protsExp_dict = cPickle.load(papers_protsExp_handle) papersTaxExp_handle = open('Uniprot-Bias/goa_taxid_exp_papers.pik', 'rb') papersTaxExp_dict = cPickle.load(papersTaxExp_handle) # going for the top fifty papers top = 50 papers_annots2_dict = sp_tools.top_papers_dict(papersExp_dict, papers_protsExp_dict, top=top) all_tt_count = sp_tools.term_types_all_papers(papersExp_dict) #takes a really long time go_ec_count = sp_tools.go_terms_with_ec_per_paper(papersExp_dict, top=top) # this takes a bit of time too GO_EC_Count_collect_tuple = sp_tools.sort_go_ec_count(go_ec_count) allEvCodes_dict = sp_tools.ev_codes_all_papers(papersExp_dict) sortedProtsPerPaper_tuple = sp_tools.sort_papers_prots(papers_protsExp_dict) sp_tools.print_paper_per_prots_sorted_go(papers_annots2_dict, all_tt_count, go_ec_count, allEvCodes_dict, sortedProtsPerPaper_tuple, "allExpPaperInfoTop50_sortedGO.txt", top=top)
papersExp_dict = cPickle.load(papersExp_handle) papers_protsExp_handle = open('goa_exp_papers_prots_lo.pik', 'rb') papers_protsExp_dict = cPickle.load(papers_protsExp_handle) # going for the top fifty papers top = 50 papers_annots2_dict = sp_tools.top_papers_dict(papersExp_dict, papers_protsExp_dict, top=top) print "really long time... (1)" all_tt_count = sp_tools.term_types_all_papers( papersExp_dict) #takes a really long time print "...done" go_ec_count = sp_tools.go_terms_with_ec_per_paper( papersExp_dict, top=top) # this takes a bit of time too allEvCodes_dict = sp_tools.ev_codes_all_papers(papersExp_dict) sortedProtsPerPaper_tuple = sp_tools.sort_papers_prots(papers_protsExp_dict) sp_tools.print_paper_per_prots_go(papers_annots2_dict, all_tt_count, go_ec_count, allEvCodes_dict, sortedProtsPerPaper_tuple, "allExpPaperInfoTop50_lo.txt", top=top) # Not experimental """papersNoExp_handle = open('goa-pickles/goa_not_exp_papers.pik', 'rb') papersNoExp_dict = cPickle.load(papersNoExp_handle) papers_protsNoExp_handle = open('goa-pickles/goa_not_exp_papers_prots.pik', 'rb') papers_protsNoExp_dict = cPickle.load(papers_protsNoExp_handle)