def get_tr_dicts_and_ids():
# Download metadata file if it is not in data directory
download_metadata()
# Get the text ref objects from the DB corresponding to the CORD19
# articles
text_refs = get_unique_text_refs()
md = get_metadata_dict()
tr_dicts, multiple_tr_ids = cord19_metadata_for_trs(text_refs, md)
return tr_dicts, multiple_tr_ids
def get_cord_info():
global _cord_by_doi
global _cord_by_pmid
if not (_cord_by_doi and _cord_by_pmid):
cord_md = get_metadata_dict()
for md_entry in cord_md:
if md_entry.get('doi'):
_cord_by_doi[md_entry['doi'].upper()] = md_entry
if md_entry.get('pubmed_id'):
_cord_by_pmid[md_entry['pubmed_id']] = md_entry
return (_cord_by_doi, _cord_by_pmid)
import re
import csv
from covid_19.preprocess import get_metadata_dict, get_zip_texts_for_entry, \
get_metadata_df, get_all_texts
from indra_db.util import get_db
covid_docs_file = '../covid_docs_ranked_corona.csv'
covid_pmids = set()
with open(covid_docs_file, 'rt') as f:
csv_reader = csv.reader(f, delimiter=',')
for row in csv_reader:
pmid = row[4]
covid_pmids.add(pmid)
md = get_metadata_dict()
aa_reg = '[ACDEFGHIKLMNPQRSTVWY]'
mut_reg = '\s+' + aa_reg + '\d+' + aa_reg + '\s+'
print(mut_reg)
aa_short = [
'ala', 'arg', 'asn', 'asp', 'cys', 'gln', 'glu', 'gly', 'his', 'ile',
'leu', 'lys', 'met', 'phe', 'pro', 'ser', 'thr', 'trp', 'tyr', 'val'
]
aa_short_reg = '|'.join([aa for aa in aa_short])
aa_seq_reg = '(?:%s)\d{2,5}' % aa_short_reg
print(aa_seq_reg)
ignore_list = (
'Y2H', # Yeast two-hybrid
'C3H', # Mouse strain