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searchPubmed.py
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searchPubmed.py
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#this is basically a script to search the pubmed by "string"
from StringIO import StringIO
from Bio import Entrez, Medline
def search_medline(query, email):
Entrez.email = email
search = Entrez.esearch(db='pubmed', term=query, usehistory='y')
handle = Entrez.read(search)
try:
return handle
except Exception as e:
raise IOError(str(e))
finally:
search.close()
def fetch_rec(rec_id, entrez_handle):
fetch_handle = Entrez.efetch(db='pubmed', id=rec_id,
rettype='Medline', retmode='text',
webenv=entrez_handle['WebEnv'],
query_key=entrez_handle['QueryKey'])
rec = fetch_handle.read()
return rec
def main(query, email):
rec_handler = search_medline(query, email)
for rec_id in rec_handler['IdList']:
rec = fetch_rec(rec_id, rec_handler)
rec_file = StringIO(rec)
medline_rec = Medline.read(rec_file)
if 'AB' in medline_rec:
print(medline_rec['AB'])
if __name__ == '__main__':
email = "deep.dhungel@fu-berlin.de"
query = "diabetes AND schizophrenia"
main(query, email)