[Biopython] Entrez.efetch issue with the returning data type
Anna Kostikova
anna.kostikova at gmail.com
Tue Feb 28 13:28:50 UTC 2012
Dear list,
Since today I've started to have an issue with Entrez.efetch utility,
and in particular with the rettype parameter. Essentially, the format
of the data returned when I specify
Entrez.efetch(db='nucleotide',id='JQ042818.1',rettype='gb') does not
correspond anymore to a genbank datatype. Few days ago all was fine.
What is going on?
the script is:
from Bio import Entrez
Entrez.email = 'my.email at domain.com'
local_file=open("test.gb", 'w')
try:
handle =
Entrez.efetch(db='nucleotide',id='JQ042818.1',rettype='gb') #download
record with Entrez.efetch
local_file.write(handle.read()) #write to a file
handle.close()
except:
print "Accsession id is not found"
local_file.close()
Thanks a lot for your ideas,
Anna
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