write output of for loop in csv python

Question

i want to write the result of for loop which is PMID = Id of litrature ,Date = date of publication ,title = title of article,Abstract = abtract of artilce in csv file but it is saving only one element of the output no all

  import numpy as np 
  from Bio import Entrez
  from Bio import Medline
  import csv
  import pandas as pd
  Entrez.email = "[email protected]"

  handle = Entrez.esearch(db="pmc", 
        term = "Antimicrobial resistance Drug Resistance",
        rettype = "medline",retmode = "txt",
        retmax= "200",sort = "pub date")

  result = Entrez.read(handle)

  handle.close()

  Id = result ['IdList']

  print (Id)

  handle2 = Entrez.efetch(db="pmc", 
    id=Id, rettype="medline", 
    retmode="text")

  records = Medline.parse(handle2)


  header = ['ID','Date','Title','Abstract']



  for result in records :

   PMID = result['PMID']
   Abstract = result['AB']
   title = result['TI']
   Date = result['DP']

   print (PMID,Date,title,Abstract)


   fields = [PMID, title,Date,Abstract]

   rows = [PMID,Date,title,Abstract]

   with open ('/home/shayez/Desktop/karim.csv','wt') as csvfile:
      writer = csv.writer(csvfile, delimiter ="\t" )
      writer.writerow(header)

      writer.writerow(rows)

  handle2.close()

Because you open the file in write mode in a loop, which wipes any contents from the previous loop. Open in append mode (though this will be really inefficient and you'll probably want to refactor the code to be able to use writerows and open the file only once) — roganjosh
– roganjosh, Commented Jan 2, 2019 at 22:17

solarc · Accepted Answer · 2019-01-02 22:21:37Z

1

You are opening the file, writing and closing it inside the loop (the with makes sure the file is closed after the with's scope is done) so it is replacing the previous file for each element in the loop.

Try opening the file only once, before the loop:

with open ('/home/shayez/Desktop/karim.csv','wt') as csvfile:
    writer = csv.writer(csvfile, delimiter ="\t" )
    writer.writerow(header)

    for result in records :
        PMID = result['PMID']
        Abstract = result['AB']
        title = result['TI']
        Date = result['DP']

        print (PMID,Date,title,Abstract)

        fields = [PMID, title,Date,Abstract]
        rows = [PMID,Date,title,Abstract]

        writer.writerow(rows)

answered Jan 2, 2019 at 22:21

solarc

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