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)
import cPickle
import sp_tools
#Experimental
papersExp_handle = open('goa_exp_papers_lo.pik', 'rb')
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
import cPickle
import sp_tools
#Experimental
papersExp_handle = open('goa-pickles/goa_exp_papers.pik', 'rb')
papersExp_dict = cPickle.load(papersExp_handle)
papers_protsExp_handle = open('goa-pickles/goa_exp_papers_prots.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)
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
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,
"FOOallExpPaperInfoTop50.txt",
top=top)
# Not experimental
"""papersNoExp_handle = open('goa-pickles/goa_not_exp_papers.pik', 'rb')
papersNoExp_dict = cPickle.load(papersNoExp_handle)
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)
#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)
import cPickle
import sp_tools
# Experimental
papersExp_handle = open("goa-pickles/goa_exp_papers.pik", "rb")
papersExp_dict = cPickle.load(papersExp_handle)
papers_protsExp_handle = open("goa-pickles/goa_exp_papers_prots.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)
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
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.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)