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write output of for loop in csv python
0
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()
python
asked Jan 2 at 22:11
Shayez KarimShayez Karim
63
add a comment |
0
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()
python
asked Jan 2 at 22:11
Shayez KarimShayez Karim
63
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 usewriterowsand open the file only once)
– roganjosh
Jan 2 at 22:17
add a comment |
0
0
0
1
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()
python
asked Jan 2 at 22:11
Shayez KarimShayez Karim
63
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()
python
python
asked Jan 2 at 22:11
Shayez KarimShayez Karim
63
asked Jan 2 at 22:11
Shayez KarimShayez Karim
63
asked Jan 2 at 22:11
Shayez KarimShayez Karim
63
asked Jan 2 at 22:11
Shayez KarimShayez Karim
63
asked Jan 2 at 22:11
Shayez KarimShayez Karim
63
63
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 usewriterowsand 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 usewriterowsand 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
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
0
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
solarcsolarc
4,26923149
add a comment |
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1 Answer
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active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
0
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
solarcsolarc
4,26923149
add a comment |
0
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
solarcsolarc
4,26923149
add a comment |
0
0
0
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
solarcsolarc
4,26923149
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
solarcsolarc
4,26923149
answered Jan 2 at 22:21
solarcsolarc
4,26923149
answered Jan 2 at 22:21
solarcsolarc
4,26923149
answered Jan 2 at 22:21
solarcsolarc
4,26923149
4,26923149
add a comment |
add a comment |
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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
writerowsand open the file only once)– roganjosh
Jan 2 at 22:17