def compare_labeled_with_categories():
categories_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/categories/"
results_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/results/"
with pmu.PubmedReader("../../data/pubmed_list/good/labeled.txt") as pr:
good_pmids = [pmid for pmid in pr.read_all()]
with pmu.PubmedReader("../../data/pubmed_list/bad/labeled.txt") as pr:
bad_pmids = [pmid for pmid in pr.read_all()]
for category in os.listdir(categories_dir):
good_pmids_result = []
bad_pmids_result = []
other_pmids_result = []
with pmu.PubmedReader("{0}{1}".format(categories_dir, category)) as pr:
for pmid in pr.read_all():
if pmid in good_pmids:
good_pmids_result.append(pmid)
elif pmid in bad_pmids:
bad_pmids_result.append(pmid)
else:
other_pmids_result.append(pmid)
with pmu.PubmedWriter("{0}{1}_good".format(results_dir, category)) as pw:
pw.write_all(good_pmids_result)
with pmu.PubmedWriter("{0}{1}_bad".format(results_dir, category)) as pw:
pw.write_all(bad_pmids_result)
with pmu.PubmedWriter("{0}{1}_other".format(results_dir, category)) as pw:
pw.write_all(other_pmids_result)
def compare_categories_with_bad_and_good():
bad_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/bad/"
good_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/good/"
rest_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/rest/"
bad_categories_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/bad_categories/"
results_good_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/results_labeled_categories/good/"
results_bad_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/results_labeled_categories/bad/"
results_rest_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/results_labeled_categories/rest/"
results_other_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/results_labeled_categories/other/"
with pmu.PubmedReader("{0}{1}".format(good_dir, "labeled.txt")) as pr:
good_list = [pmid for pmid in pr.read_all()]
with pmu.PubmedReader("{0}{1}".format(bad_dir, "labeled.txt")) as pr:
bad_list = [pmid for pmid in pr.read_all()]
with pmu.PubmedReader("{0}{1}".format(rest_dir, "all")) as pr:
rest_list = [pmid for pmid in pr.read_all()]
good_results = {}
bad_results = {}
rest_results = {}
other_results = {}
for bad_category in os.listdir(bad_categories_dir):
good_results[bad_category] = []
bad_results[bad_category] = []
rest_results[bad_category] = []
other_results[bad_category] = []
with pmu.PubmedReader("{0}{1}".format(bad_categories_dir, bad_category)) as pr:
for pmid in pr.read_all():
if pmid in good_list:
good_results[bad_category].append(pmid)
elif pmid in bad_list:
bad_results[bad_category].append(pmid)
elif pmid in rest_list:
rest_results[bad_category].append(pmid)
else:
other_results[bad_category].append(pmid)
create_dir(results_good_dir)
for good_key, good_value in good_results.items():
with pmu.PubmedWriter("{0}{1}".format(results_good_dir, good_key)) as pr:
pr.write_all(good_value)
create_dir(results_bad_dir)
for bad_key, bad_value in bad_results.items():
with pmu.PubmedWriter("{0}{1}".format(results_bad_dir, bad_key)) as pr:
pr.write_all(bad_value)
create_dir(results_rest_dir)
for rest_key, rest_value in rest_results.items():
with pmu.PubmedWriter("{0}{1}".format(results_rest_dir, rest_key)) as pr:
pr.write_all(rest_value)
create_dir(results_other_dir)
for other_key, other_value in other_results.items():
with pmu.PubmedWriter("{0}{1}".format(results_other_dir, other_key)) as pr:
pr.write_all(other_value)
def compare_categories_with_bad_categories():
bad_categories_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/bad_categories/"
groups_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/results/"
results_bad_categories_dir = "/home/pjarnot/polsl/conference/biohackathon/Pharmacology/data/pubmed_list/results_bad_categories/"
groups = {}
results_bad_categories = {}
init_results_bad_categories_dict(bad_categories_dir, groups_dir, results_bad_categories)
init_groups_dict(groups_dir, groups)
create_dir("{0}".format(results_bad_categories_dir))
for bad_category in os.listdir(bad_categories_dir):
create_dir("{0}{1}".format(results_bad_categories_dir, bad_category))
with pmu.PubmedReader("{0}{1}".format(bad_categories_dir, bad_category)) as pr:
for pmid in pr.read_all():
for group_key, group_value in groups.items():
if pmid in group_value:
results_bad_categories[bad_category][group_key].append(pmid)
for bad_category_key, bad_category_value in results_bad_categories.items():
for group_key, group_value in results_bad_categories[bad_category_key].items():
with pmu.PubmedWriter("{0}{1}/{2}".format(results_bad_categories_dir, bad_category_key, group_key)) as pr:
pr.write_all(results_bad_categories[bad_category_key][group_key])
def read_pmids(options):
with pmu.PubmedReader(options.input) as pmr:
return [pmid for pmid in pmr.read_all()]
def init_groups_dict(groups_dir, groups):
for group in os.listdir(groups_dir):
with pmu.PubmedReader("{0}{1}".format(groups_dir, group)) as pr:
groups[group] = [pmid for pmid in pr.read_all()]
import src.utils.pubmedutils as pmu
if __name__ == '__main__':
with pmu.PubmedReader("../../data/pubmed_list/good/labeled.txt") as pr:
good_pmids = [pmid for pmid in pr.read_all()]
bad_pmids = []
with pmu.PubmedReader("../../data/pubmed_list/reviewed/list_pmid") as pr:
for pmid in pr.read_all():
if pmid not in good_pmids:
bad_pmids.append(pmid)
with pmu.PubmedWriter("../../data/pubmed_list/bad/labeled.txt") as pw:
pw.write_all(bad_pmids)