[Biopython] Fetching fasta sequences by accession number

[Patrick Kunzmann]

Hi Ahmad,

I am not sure, if Biopython is able to do this, but Biotite (a package, 
I am currently developing) can handle it.

If you want to multiple files you can use 
/biotite.database.entrez.fetch()/ 
(http://www.biotite-python.org/apidoc/biotite.database.entrez/fetch.html).

If you want all sequences in a single file you can use 
/biotite.database.entrez.fetch_single_file()/ 
(http://www.biotite-python.org/apidoc/biotite.database.entrez/fetch_single_file.html).


Example:

import biotite.database.entrez as entrez

file_name = entrez.fetch_single_file(["M95099"," M95098"], "test.fasta", 
db_name="nuccore", ret_type="fasta")


Best regards

Patrick



On 20.04.2018 13:25, Ahmad Abdelzaher wrote:
> How can I batch download fasta sequences by accession number? Is there 
> a Biopython method that can do that? Any other suggestions or 
> alternatives?
>
> Regards.
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython

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