count = 0

with open(input_file, 'rb') as f:

lines = f.readlines()

for line in lines:

count = count + 1

line = line.strip()

line = removeNonAscii(line) # metamap does not support non-ascii characters

extract_pairs = open(output_file, "w")

extract_pairs.write("input\tscore\tconcept_id\tconcept_name\tconcept_type\n")

count = 0

with open(input_file, 'rb') as f:

reader = f.readlines()

for record in reader:

count = count + 1

candidate_dzs = []

try:

with open(temp_file + str(count) + '.txt', "r") as f1:

lines = f1.readlines()

for line in lines:

line = line.strip()

if (line.find('[Disease or Syndrome]')>0):

line = line.replace('[Disease or Syndrome]','')

type = "Disease or Syndrome"

elif (line.find('[Neoplastic Process]')>0):

line = line.replace('[Neoplastic Process]','')

type = "Neoplastic Process"

elif (line.find('[Sign or Symptom]')>0):

line = line.replace('[Sign or Symptom]','')

type = "Sign or Symptom"

else:

continue

#get the score

score = (line[0:line.find(" ")].strip()).strip()

concept_id = (line[line.find(" "):].split(":")[0]).replace(" E ","").strip()

concept_name = (line[line.find(" "):].split(":")[1]).strip()

candidate_dzs.append(str(score) + "\t" + concept_id + "\t" + concept_name + "\t" + type)

except IOError:

print 'no file found for ' + str(count)

#remove the redunct

candidate_dzs = Set(candidate_dzs)

for candidate_dz in candidate_dzs:

extract_pairs.write( record.strip() + "\t" + candidate_dz + "\n")