Attachment 'pubmed.py'

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   1 from Bio import Entrez
   2 from Bio import Medline
   3 
   4 author=raw_input("Enter author name: ")
   5 
   6 # The following line MUST contain your valid email address
   7 Entrez.email = "user@bcm.edu"     
   8 
   9 # Do a pubmed query to find all papers by a specific author
  10 handle = Entrez.esearch(db="pubmed", term="{}[Author]".format(author), retmax=500)
  11 record = Entrez.read(handle)
  12 handle.close()
  13 
  14 # record is a dictionary-like object. IdList is a list of pubmedid numbers matching the query
  15 ids=record["IdList"]
  16 
  17 # fetch all of the records in the list of matching ids
  18 handle=Entrez.efetch(db="pubmed",id=tuple(ids),rettype="medline")
  19 records = list(Medline.parse(handle))
  20 handle.close()
  21 
  22 # find all unique coauthors
  23 coauth=set()
  24 for r in records: 
  25 	coauth.update(r["AU"])
  26 
  27 print "Coauthors:",coauth
  28 print len(ids)," matching records"
  29 print len(coauth)," coauthors"

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