import sys import datetime # USAGE: # python ./print_Top50ProtsPMIDperTaxonID.py > Top50ProtsPMIDperTaxonID.log 2>&1 d = datetime.date.today() finalOutputFile = "Top50ProtSpeciesWithTop50AnnotPapers." + str(d) + ".tsv" taxonIDFile = "Uniprot-Bias/handTax50list.txt" # load up the pre-pickled data print "load up the pre-pickled data" # 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) # papersExp_handle = open('Uniprot-Bias/goa_exp_papers.pik', 'rb') # papersExp_dict = cPickle.load(papersExp_handle) ncbi_paper_handle = open("Uniprot-Bias/ncbi_paper_info.pik") ncbi_paper_dict = cPickle.load(ncbi_paper_handle) # Print out PMID info per TaxonID top = 50 pmidTaxonIDs_dict = sp_tools.count_PMID_in_taxonID(papersTaxExp_dict) # papers_annots2_dict = sp_tools.top_papers_dict(papersExp_dict, papers_protsExp_dict, top=500) sp_tools.print_papers_from_TaxonID_list( taxonIDFile, pmidTaxonIDs_dict, ncbi_paper_dict, finalOutputFile, papersTaxExp_dict, True, top )
#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) #Print out PMID info per TaxonID top = 50 pmidTaxonIDs_dict = sp_tools.count_PMID_in_taxonID(papersTaxExp_dict) papers_annots2_dict = sp_tools.top_papers_dict(papersExp_dict, papers_protsExp_dict, top=500) taxonIDFile = 'Uniprot-Bias/handTax50list.txt' sp_tools.print_papers_from_TaxonID_list(taxonIDFile, pmidTaxonIDs_dict, papers_annots2_dict, "AllPMIDvTaxonIDsTop50.txt", papersExp_dict, True, top) #count all the annotations & the annotations per Ev Code allECCode_dict = sp_tools.count_all_annotations_per_ec(papersExp_dict) # count all the term type annotations sum_tt_count = sp_tools.count_all_term_types(papersExp_dict) # count all the species annotations all_taxonID_dict = sp_tools.count_all_annotations_taxonIDs(papersTaxExp_dict) #top go codes