[Biopython] Fwd: Biopython post from kingaram at hanmail.net requires approval

Peter biopython at maubp.freeserve.co.uk
Fri Aug 28 10:16:52 UTC 2009


Hi all,

I have just forwarded the following message to the list as
it had been blocked with a "suspicious header". Could I
remind people please try and send "plain text" emails,
rather than rich HTML formatting with pictures etc as
these are likely to get blocked by the mailing list.

Thanks

Peter

---------- Forwarded message ----------
From: "titt" <kingaram at hanmail.net>
To: <biopython at biopython.org>
Date: Fri, 28 Aug 2009 09:42:03 +0900 (KST)
Subject: Finding protein ID using Entrez.efetch

Hi all,

I'm looking for the way to extract the data of protein ID numbers in
the Genbank. I got my Genbank data and save it as a xml file using
this commend.

from Bio import Entrez
handle=Entrez.efetch(db="nuccore",id="256615878",rettype="gb")
record=handle.read()
save_file = open("record.xml","w")
save_file.write(record)
save_file.close()

What I need is all the protein ID (For example: EEU21068.1) or GI
number (for example: 256615878) in this Genbank page for the blast
search. Could you let me know how to extract these information, save
in some format, and use them?

Thank you,
Ar! am




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