[Biopython] Fetching fasta sequences by accession number
Iddo Friedberg
idoerg at gmail.com
Fri Apr 20 14:16:01 UTC 2018
There is an example here for downloading multiple GenBank entries:
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc131
Depending on the actual database you are downloading from, you can use
rettype="fasta" or convert a genbank file to fasta as in here:
http://biopython.org/wiki/Converting_sequence_files
The possible rettype and retmode are dependent on the database you are
fetching from, and determined of the efetch API . More about that here:
https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
HTH,
Iddo
On Fri, Apr 20, 2018 at 6:25 AM, Ahmad Abdelzaher <underoath006 at gmail.com>
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.
>
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> Biopython mailing list - Biopython at mailman.open-bio.org
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>
--
Iddo Friedberg
http://iddo-friedberg.net/contact.html
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