def output_parser(outdir, prefix):
'''output: article obj list'''
tm_tk = outdir + '/' + prefix + '.tmvarI.tk.PubTator'
tm_ab = outdir + '/' + prefix + '.tmvarI.abstract.PubTator'
tm_re = outdir + '/' + prefix + '.tmvarI.results.PubTator'
dn_tk = outdir + '/' + prefix + '.DNormO.tk'
dn_ab = outdir + '/' + prefix + '.DNormO.abstract'
dn_re = outdir + '/' + prefix + '.DNormO.results'
gn_dir = outdir + '/' + prefix + '.GNormPlusO'
articles = []
for pmid, string, mutation_entry_ls in tmvar_parser(tm_tk):
article_obj = Base.Article(pmid) # create article_obj
tk_obj = Base.TK(string) # create tk_obj
for e in mutation_entry_ls:
tk_obj.add_e(e) # add entry
article_obj.add_tk(tk_obj)
articles.append(article_obj)
# abstract
for pmid, string, mutation_entry_ls in tmvar_parser(tm_ab):
article_obj = found_article(pmid, articles) # found article_obj
abstract_obj = Base.Abstract(string) # create abstract_obj
for e in mutation_entry_ls:
abstract_obj.add_e(e) # add entry
article_obj.add_abstract(abstract_obj)
# results
for pmid, string, mutation_entry_ls in tmvar_parser(tm_re):
article_obj = found_article(pmid, articles) # found article_obj
results_obj = Base.Results(string) # create tk_obj
for e in mutation_entry_ls:
results_obj.add_e(e) # add entry
article_obj.add_results(results_obj)
# DNorm
for pmid, entry in DNorm_parser(dn_tk):
article_obj = found_article(pmid, articles)
article_obj.tk.add_e(entry)
for pmid, entry in DNorm_parser(dn_ab):
article_obj = found_article(pmid, articles)
article_obj.abstract.add_e(entry)
for pmid, entry in DNorm_parser(dn_re):
article_obj = found_article(pmid, articles)
article_obj.results.add_e(entry)
# GNormPlus
for pmid, entry, fn in GNormPlus_parser(gn_dir):
article_obj = found_article(pmid, articles)
if re.search('tk', fn):
article_obj.tk.add_e(entry)
elif re.search('abstract', fn):
article_obj.abstract.add_e(entry)
else:
article_obj.results.add_e(entry)
return articles
def output_parser(outdir, prefix):
'''output: article obj list'''
tm_tk = outdir + '/' + prefix + '.tmvarI.tk.PubTator'
tm_ab = outdir + '/' + prefix + '.tmvarI.abstract.PubTator'
tm_re = outdir + '/' + prefix + '.tmvarI.results.PubTator'
dn_tk = outdir + '/' + prefix + '.DNormO.tk'
dn_ab = outdir + '/' + prefix + '.DNormO.abstract'
dn_re = outdir + '/' + prefix + '.DNormO.results'
gn_tk = outdir + '/' + prefix + '.GNormPlusO.tk'
gn_ab = outdir + '/' + prefix + '.GNormPlusO.abstract'
gn_re = outdir + '/' + prefix + '.GNormPlusO.results'
emu_tk = outdir + '/EMU_1.19_HUGO_' + prefix + '.EMU.tk'
emu_ab = outdir + '/EMU_1.19_HUGO_' + prefix + '.EMU.abstract'
emu_re = outdir + '/EMU_1.19_HUGO_' + prefix + '.EMU.results'
articles = []
for pmid, string, mutation_entry_ls in var_parser(tm_tk, emu_tk):
article_obj = Base.Article(pmid) # create article_obj
tk_obj = Base.TK(string) # create tk_obj
for e in mutation_entry_ls:
tk_obj.add_e(e) # add entry
article_obj.add_tk(tk_obj)
articles.append(article_obj)
# abstract
for pmid, string, mutation_entry_ls in var_parser(tm_ab, emu_ab):
article_obj = found_article(pmid, articles) # found article_obj
abstract_obj = Base.Abstract(string) # create abstract_obj
for e in mutation_entry_ls:
abstract_obj.add_e(e) # add entry
article_obj.add_abstract(abstract_obj)
# results
has_results = True
try:
for pmid, string, mutation_entry_ls in var_parser(tm_re, emu_ab):
article_obj = found_article(pmid, articles) # found article_obj
results_obj = Base.Results(string) # create tk_obj
for e in mutation_entry_ls:
results_obj.add_e(e) # add entry
article_obj.add_results(results_obj)
except FileNotFoundError as e:
has_results = False
print('no results: {0}'.format(e))
# DNorm
for pmid, entry in DNorm_parser(dn_tk):
article_obj = found_article(pmid, articles)
article_obj.tk.add_e(entry)
for pmid, entry in DNorm_parser(dn_ab):
article_obj = found_article(pmid, articles)
article_obj.abstract.add_e(entry)
if has_results:
for pmid, entry in DNorm_parser(dn_re):
article_obj = found_article(pmid, articles)
article_obj.results.add_e(entry)
# GNormPlus
for pmid, entry in GNormPlus_parser(gn_tk):
article_obj = found_article(pmid, articles)
article_obj.tk.add_e(entry)
for pmid, entry in GNormPlus_parser(gn_ab):
article_obj = found_article(pmid, articles)
article_obj.abstract.add_e(entry)
if has_results:
for pmid, entry in GNormPlus_parser(gn_re):
article_obj = found_article(pmid, articles)
article_obj.results.add_e(entry)
'''sort entry'''
for i in articles:
if i.abstract: # possible no abstract
i.abstract.sort_entry()
if i.results: # possible no results
i.results.sort_entry()
pass
return articles
