encoding="utf-8")
counter = {}
for line in file.iter():
drug = line[3]
drug = drug.split(";")[0]
if drug:
if drug not in counter:
counter[drug] = 1
else:
counter[drug] += 1
print(counter)
print(len(counter))
s = sorted(counter.items(), key=lambda x: x[1])[::-1]
print(s)
save_file = FM("../PUBMED_DATA/drug_counter", extension=".txt")
fp = save_file.get_filepointer()
for i in s:
fp.write(("\t".join([i[0], str(i[1])]) + '\n'))
fp.close()
# with open("../PUBMED_DATA/drug_counter.latest.txt", 'w', encoding = "utf8") as fp:
# for i in s:
# fp.write(("\t".join([i[0],str(i[1])])+'\n'))
else:
match[pmid] = (year, title, match[pmid][2] , description)
# tf.step()
missing= 0
for k,v in match.items():
if v==("","",[],""):
missing+=1
pubmedNdrugs = FM("../PUBMED_DATA/pubmed2606_with_drugs",
extension = ".txt", olddata_dir = "../OLD_DATA/PUBMED_DATA/")
with pubmedNdrugs.get_filepointer() as fp:
for k,v in match.items():
if v[2]:
res = ""
for i in range(len(v[2])):
v[2][i] = ";".join(v[2][i])
topop = []
for i in v[2]:
for j in v[2]:
# " " not in j.replace(i, "") and not " "+i+" " in v[1]
if i in j and len(i) < len(j) and i not in topop and "-" in j.replace(i, "") and not v[1].count(i)>1:
topop.append(i)
for to in topop:
v[2].pop(v[2].index(to))
tree = ET.parse('../DRUGBANK/drugbank_db_schema.xml')
root = tree.getroot()
res = []
def tree_builder(node,depth):
for child in node:
print(child.tag)
res.append(depth * '\t' + child.tag)
tree_builder(child, depth+1)
tree_builder(root, 0)
tree_tagging = FM("../DRUGBANK/tree_tagging", extension = ".txt")
with tree_tagging.get_filepointer() as fp:
for t in res:
fp.write(t+'\n')
fp.close()
# def tree_builder(node):
# children = []
# for elem in node:
# children.append(elem.tag)
# next_elem = tree_builder(elem)
# if next_elem:
# children.append(next_elem)
# return children
pool.append(item)
# #Build final result from pool
while pool:
elems = pool.pop()
res = []
while elems:
searching = elems.pop()
if searching not in res:
res.append(searching)
for p in pool:
if searching in p:
for i in p:
elems.append(i)
indices = [i for i, x in enumerate(pool) if x == p]
pool = [x for i, x in enumerate(pool) if i not in indices]
final_ref.append(sorted(res))
csv = []
for i in final_ref:
csv.append(";".join(i))
csv = list(set(csv))
csv.sort()
full_drug_list = FM("../DRUG_LISTS/full_drug_list", extension=".txt")
with full_drug_list.get_filepointer() as fp:
for drug in csv:
fp.write(drug + "\n")
fp.close()
from utils import File_Maker as FM
file = FM("GRAPH/test78324264.txt", replace_old=True, version_control=False)
print(file.get_filename())
print(file.get_extension())
print(file.get_savedir())
print(file.original_dir)
fp = file.get_filepointer()
fp.write("adzaf")
fp.write("sth")
fp.write("rthter")
fp.write("rthet")
fp.close()