write output of for loop in csv python

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 = "shayezkarimcide@gmail.com"



  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()

asked Jan 2 at 22:11

Shayez Karim

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
Jan 2 at 22:17

add a comment |

  import numpy as np 

  from Bio import Entrez

  from Bio import Medline

  import csv

  import pandas as pd

  Entrez.email = "shayezkarimcide@gmail.com"



  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()

asked Jan 2 at 22:11

Shayez Karim

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
Jan 2 at 22:17

add a comment |

  import numpy as np 

  from Bio import Entrez

  from Bio import Medline

  import csv

  import pandas as pd

  Entrez.email = "shayezkarimcide@gmail.com"



  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()

asked Jan 2 at 22:11

Shayez Karim

  import numpy as np 

  from Bio import Entrez

  from Bio import Medline

  import csv

  import pandas as pd

  Entrez.email = "shayezkarimcide@gmail.com"



  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()

python

asked Jan 2 at 22:11

Shayez Karim

asked Jan 2 at 22:11

Shayez Karim

asked Jan 2 at 22:11

Shayez Karim

asked Jan 2 at 22:11

Shayez Karim

asked Jan 2 at 22:11

Shayez Karim

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
Jan 2 at 22:17

add a comment |

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
Jan 2 at 22:17

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
Jan 2 at 22:17

add a comment |

1 Answer
1

active

oldest

votes

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 at 22:21

solarc

4,26923149

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1 Answer
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active

oldest

votes

1 Answer
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active

oldest

votes

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 at 22:21

solarc

4,26923149

add a comment |

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 at 22:21

solarc

4,26923149

add a comment |

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 at 22:21

solarc

4,26923149

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 at 22:21

solarc

4,26923149

answered Jan 2 at 22:21

solarc

4,26923149

answered Jan 2 at 22:21

solarc

4,26923149

answered Jan 2 at 22:21

solarc

4,26923149

add a comment |

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