[Biopython-dev] Notification: incoming/112

biopython-bugs at bioperl.org biopython-bugs at bioperl.org
Sat Dec 28 09:10:34 EST 2002


JitterBug notification

new message incoming/112

Message summary for PR#112
	From: oeed at online.no
	Subject: Problem: Documentation of PubMed
	Date: Sat, 28 Dec 2002 09:10:29 -0500
	0 replies 	0 followups

====> ORIGINAL MESSAGE FOLLOWS <====

>From oeed at online.no Sat Dec 28 09:10:33 2002
Received: from localhost (localhost [127.0.0.1])
	by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id gBSEATSQ016570
	for <biopython-bugs at pw600a.bioperl.org>; Sat, 28 Dec 2002 09:10:33 -0500
Date: Sat, 28 Dec 2002 09:10:29 -0500
Message-Id: <200212281410.gBSEATSQ016570 at pw600a.bioperl.org>
From: oeed at online.no
To: biopython-bugs at bioperl.org
Subject: Problem: Documentation of PubMed
X-Spam-Status: No
X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang)

Full_Name: Øyvind Edvardsen
Module: Medline/PubMed documentation
Version: 1.10
OS: linux and winxp
Submission from: kunde1936.tromso.alfanett.no (62.16.135.165)


I was trying to exploit the PubMed stuff and
followed the Cookbook available from the documentation page. No success!
The problem is the import stuff:
in all the docs I found it is shown as
from Bio.Medline import PubMed
from Bio import Medline
but what really works is:
from Bio import PubMed
from Bio.PubMed import Medline
After those imports a parser and dict can
be set up just as in the example code in the Cookbook. And it works very good!

Maybe the docs went out of sync with the code
some time ago...

Anyway, this stuff should be fixed in the docs
so that other people can use biopython's Medline without having to figure out
what's wrong first.

OED.





More information about the Biopython-dev mailing list