Biopython, entrez.efetch, how to get results file

[umnklang]

I used the following code to get the annotations from GeneID's

handle = Entrez.efetch(db="gene", id="6485345,6484180,6482845", rettype="gene_table", retmode="text")

can anyone help with getting these results as a text file?

[maubp]

The Biopython Tutorial does cover this: http://biopython.org/DIST/docs/tutorial/Tutorial.html

The simplest way would be something like this - read the data into a string, write it to a file:

from Bio import Entrez

net_handle = Entrez.efetch(db="gene", id="6485345,6484180,6482845", rettype="gene_table", retmode="text")
data = net_handle.read()
net_handle.close()

out_handle = open("my_file.txt", "w")
out_handle.write(data)
out_handle.close()

For larger files you may not want to keep the whole thing in memory, so writing it line by line would be better:

from Bio import Entrez

net_handle = Entrez.efetch(db="gene", id="6485345,6484180,6482845", rettype="gene_table", retmode="text")
out_handle = open("my_file.txt", "w")

for line in net_handle:
    out_handle.write(line)

out_handle.close()
net_handle.close()