downloading full genbank file using Entrez efetch
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11 months ago
seok1213neo ▴ 20

I am trying to download the full complete genbank file (where it has all the sequences)

using biopython Entrez module.

so far I am writing like the below

with Entrez.efetch (db = "nucleotide", rettype = 'gb', id = "NC_000853.1", retmode = 'text') as gb_file:

but it only seems to download the short version of genbank file.

how should i modify the code so i can downloade the full version of genbank file?

genbank full genbank entrez efetch • 1.0k views
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Entering edit mode

I don't know if this is possible. I tried your code and I obtained the same as it appears in the NCBI/Genbak site: https://www.ncbi.nlm.nih.gov/nuccore/NC_000853.1/. If you are interested in the whole genome or part of it use a different query.

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11 months ago
vkkodali ★ 2.8k

You need to use rettype = 'gbwithparts' to download the entire record. For more details, see Table 1 in the EFetch documentation

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