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
