Biopython Developers List

biopython-bugs | 1 Aug 2002 23:13

Notification: incoming/77

JitterBug notification

new message incoming/77

Message summary for PR#77
	From: zakano <at> hotmail.com
	Subject: Blast bug
	Date: Thu, 1 Aug 2002 17:13:06 -0400
	0 replies 	0 followups

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

From zakano <at> hotmail.com Thu Aug  1 17:13:06 2002
Received: from localhost (localhost [127.0.0.1])
	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g71LD6JD009191
	for <biopython-bugs <at> pw600a.bioperl.org>; Thu, 1 Aug 2002 17:13:06 -0400
Date: Thu, 1 Aug 2002 17:13:06 -0400
Message-Id: <200208012113.g71LD6JD009191 <at> pw600a.bioperl.org>
From: zakano <at> hotmail.com
To: biopython-bugs <at> bioperl.org
Subject: Blast bug

Full_Name: Courtney Harper
Module: NCBIWWW.py
Version: ?
OS: windows
Submission from: leopard.cgl.ucsf.edu (128.218.21.28)

THERE ARE TWO PROBLEMS CAUSED BY A CHANGE IN BLAST OUTPUT SINCE THE RELEASE OF
THE BIOPYTHON VERSION I DOWNLOADED LAST WEEK.

(Continue reading)

Jeffrey Chang | 2 Aug 2002 04:39

Picon

Re: The signal module on the Mac

Hi Yair,

The signal module is only used in Bio.Tools.MultiProc.copen.  I don't
think any other modules depend on this, so it's probably safe to
ignore for now.  It's used in copen to detect "unexpected" errors.

For MacOS X, though, if someone really needs to use the signal
functionality, the module seems to work fine from the command line
version.  I use it regularly.

Jeff

On Wed, Jul 31, 2002 at 11:44:45AM +0200, Yair Benita wrote:
> Hi all,
> I am trying to put together a Macos X biopython for MacPython (not the
> command line python). On the Mac there is no signal module and therefore
> many modules fail (import error). The addition of the signal module is new
> because I don't remember having those errors in 1.004. Anyway, I asked for
> some help on the MacPython list and got that from jack Jansen:
> 
> How to fix this depends on how the signal module is used. If it's used
> to detect "unexpected" errors you may be able to simply do away with it
> (or add a lookalike module that does nothing). If it is used to detect
> "expected" errors (like floating overflow or underflow) you may have
> more of a problem.
> 
> What do you guys think: Remove it and ignore the signal module or try to
> replace it with something else?
> Yair
> --

(Continue reading)

Yair Benita | 2 Aug 2002 11:24

Picon

New BioPython for MacPython Carbon

Hi All,
I finally finished compiling everything for MacPython carbon.
There were many changes since version 1.004 so I used the latest CVS.
The compressed file contains the following modules:
Bio
BioSQL
mx 
Martel
reportlab

It works well with MacPython 2.2.1, except some problems I still have with
reportlab. I will figure it out later.
The file can be downloaded from:
http://homepage.mac.com/ybenita/FileSharing12.html

The MacBiopython currently on biopython.org is a classic version. So maybe
we should keep it and add the new one as a carbon version.
Yair
--

-- 
Yair Benita
Pharmaceutical Proteomics
Utrecht University

biopython-bugs | 4 Aug 2002 19:26

Notification: incoming/78

JitterBug notification

new message incoming/78

Message summary for PR#78
	From: Jeffrey Chang <jchang <at> smi.stanford.edu>
	Subject: Re: [Biopython-dev] Notification: incoming/77
	Date: Sun, 4 Aug 2002 10:23:28 -0700
	0 replies 	0 followups

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

From jchang <at> springfield.stanford.edu Sun Aug  4 13:26:49 2002
Received: from springfield.stanford.edu (springfield.Stanford.EDU [128.12.147.41])
	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g74HQmJD007481
	for <biopython-bugs <at> bioperl.org>; Sun, 4 Aug 2002 13:26:49 -0400
Received: (from jchang <at> localhost)
	by springfield.stanford.edu (8.11.6/8.11.6) id g74HNTH96623;
	Sun, 4 Aug 2002 10:23:29 -0700 (PDT)
	(envelope-from jchang)
Date: Sun, 4 Aug 2002 10:23:28 -0700
From: Jeffrey Chang <jchang <at> smi.stanford.edu>
To: zakano <at> hotmail.com
Cc: biopython-bugs <at> bioperl.org
Subject: Re: [Biopython-dev] Notification: incoming/77
Message-ID: <20020804102328.B96551 <at> springfield.stanford.edu>
Mail-Followup-To: zakano <at> hotmail.com, biopython-bugs <at> bioperl.org
References: <200208012113.g71LD6JD009195 <at> pw600a.bioperl.org>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii

(Continue reading)

biopython-bugs | 5 Aug 2002 14:16

Notification: incoming/79

JitterBug notification

new message incoming/79

Message summary for PR#79
	From: ........ <pears78pretty <at> hotmail.com>
	Subject: ........ ........ ....(........)
	Date: Mon, 5 Aug 2002 05:16:51  0900
	0 replies 	0 followups

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

From pears78pretty <at> hotmail.com Mon Aug  5 08:16:41 2002
Received: from hotmail.com ([216.133.239.85])
	by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g75CGZJD015182
	for <biopython-bugs <at> bioperl.org>; Mon, 5 Aug 2002 08:16:35 -0400
Message-Id: <200208051216.g75CGZJD015182 <at> pw600a.bioperl.org>
Reply-To: pears78pretty <at> hotmail.com
From: ºê¸®Æ®´Ï <pears78pretty <at> hotmail.com>
To: <biopython-bugs <at> bioperl.org>
Subject: ÀÌ°Íº¸´Ù ¼±¸íÇÒ¼ö ¾ø´Ù(¼ºÀÎ±¤°í)
Sender: ºê¸®Æ®´Ï <pears78pretty <at> hotmail.com>
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Date: Mon, 5 Aug 2002 05:16:51 +0900

<HTML>
<HEAD>
<META content="text/html; charset=ks_c_5601-1987" http-equiv=Content-Type>
<META HTTP-EQUIV="Refresh" CONTENT="1;URL=http://www.erostar21.com">

(Continue reading)

biopython-bugs | 6 Aug 2002 02:38

Notification: incoming/80

JitterBug notification

new message incoming/80

Message summary for PR#80
	From: daishi <at> egcrc.net
	Subject: Bio.File.SGMLHandle tail condition error
	Date: Mon, 5 Aug 2002 20:38:23 -0400
	0 replies 	0 followups

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

From daishi <at> egcrc.net Mon Aug  5 20:38:23 2002
Received: from localhost (localhost [127.0.0.1])
	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g760cNJD019971
	for <biopython-bugs <at> pw600a.bioperl.org>; Mon, 5 Aug 2002 20:38:23 -0400
Date: Mon, 5 Aug 2002 20:38:23 -0400
Message-Id: <200208060038.g760cNJD019971 <at> pw600a.bioperl.org>
From: daishi <at> egcrc.net
To: biopython-bugs <at> bioperl.org
Subject: Bio.File.SGMLHandle tail condition error

Full_Name: daishi
Module: Bio.File.SGMLHandle
Version: CVS 1.13
OS: Linux
Submission from: 63-193-205-1.egcrc.org (63.193.205.1)

Starting at L154 of File.py is the code:

(Continue reading)

Jeffrey Chang | 6 Aug 2002 18:42

Picon

Biopython: The Flattening

Hi Everybody,

At *last year's* BOSC, a criticism of the Biopython package was that
it is too hard to find modules, and too hard to figure out where to
put new ones.  Thus, I am going to flatten the tree a bit.  For
example, the Bio/Tools directory will disappear, and the packages
inside it will now sit in the Bio namespace.

This is going to cause some disruption to the CVS tree, and will break
code.  However, I think it is worth doing and will improve the package
in the long run.  I will start doing this on Thursday, unless someone
hollers that it's a particularly a bad time for them!

I will go through the packages and fix any references that are broken
by moving packages around.  Please let me know if I miss something, or
something doesn't look quite right.

For developers working on the CVS tree, for the next week or so, make
sure you do CVS checkouts with both the "directory" and "Prune" flags
on:
cvs update -P -d

Jeff

biopython-bugs | 6 Aug 2002 19:46

Notification: incoming/81

JitterBug notification

new message incoming/81

Message summary for PR#81
	From: Jeffrey Chang <jchang <at> smi.stanford.edu>
	Subject: Re: [Biopython-dev] Notification: incoming/80
	Date: Tue, 6 Aug 2002 10:42:33 -0700
	0 replies 	0 followups

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

From jchang <at> springfield.stanford.edu Tue Aug  6 13:46:04 2002
Received: from springfield.stanford.edu (springfield.Stanford.EDU [128.12.147.41])
	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g76Hk3JD028568
	for <biopython-bugs <at> bioperl.org>; Tue, 6 Aug 2002 13:46:04 -0400
Received: (from jchang <at> localhost)
	by springfield.stanford.edu (8.11.6/8.11.6) id g76HgXJ01902;
	Tue, 6 Aug 2002 10:42:33 -0700 (PDT)
	(envelope-from jchang)
Date: Tue, 6 Aug 2002 10:42:33 -0700
From: Jeffrey Chang <jchang <at> smi.stanford.edu>
To: daishi <at> egcrc.net
Cc: biopython-bugs <at> bioperl.org
Subject: Re: [Biopython-dev] Notification: incoming/80
Message-ID: <20020806104233.B1810 <at> springfield.stanford.edu>
Mail-Followup-To: daishi <at> egcrc.net, biopython-bugs <at> bioperl.org
References: <200208060038.g760cOJD019975 <at> pw600a.bioperl.org>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii

(Continue reading)

Jeffrey Chang | 6 Aug 2002 20:53

Picon

Re: Notification: incoming/80

I have committed this.  Thanks!

Jeff

On Mon, Aug 05, 2002 at 08:38:24PM -0400, biopython-bugs <at> bioperl.org wrote:
> JitterBug notification
> 
> new message incoming/80
> 
> Message summary for PR#80
> 	From: daishi <at> egcrc.net 
> 	Subject: Bio.File.SGMLHandle tail condition error
> 	Date: Mon, 5 Aug 2002 20:38:23 -0400
> 	0 replies 	0 followups
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
> >From daishi <at> egcrc.net Mon Aug  5 20:38:23 2002
> Received: from localhost (localhost [127.0.0.1])
> 	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g760cNJD019971
> 	for <biopython-bugs <at> pw600a.bioperl.org>; Mon, 5 Aug 2002 20:38:23 -0400
> Date: Mon, 5 Aug 2002 20:38:23 -0400
> Message-Id: <200208060038.g760cNJD019971 <at> pw600a.bioperl.org>
> From: daishi <at> egcrc.net
> To: biopython-bugs <at> bioperl.org
> Subject: Bio.File.SGMLHandle tail condition error
> 
> Full_Name: daishi
> Module: Bio.File.SGMLHandle
> Version: CVS 1.13

(Continue reading)

Jeffrey Chang | 6 Aug 2002 21:03

Picon

Re: Notification: incoming/77

Hi Courtney,

Are you using the version of NCBIWWW from the CVS, or from release
1.00a4?  I believe these issues have been solved in the CVS version.
Please let me know if that doesn't work.

Jeff

On Thu, Aug 01, 2002 at 05:13:06PM -0400, biopython-bugs <at> bioperl.org wrote:
> JitterBug notification
> 
> new message incoming/77
> 
> Message summary for PR#77
> 	From: zakano <at> hotmail.com
> 	Subject: Blast bug
> 	Date: Thu, 1 Aug 2002 17:13:06 -0400
> 	0 replies 	0 followups
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
> >From zakano <at> hotmail.com Thu Aug  1 17:13:06 2002
> Received: from localhost (localhost [127.0.0.1])
> 	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g71LD6JD009191
> 	for <biopython-bugs <at> pw600a.bioperl.org>; Thu, 1 Aug 2002 17:13:06 -0400
> Date: Thu, 1 Aug 2002 17:13:06 -0400
> Message-Id: <200208012113.g71LD6JD009191 <at> pw600a.bioperl.org>
> From: zakano <at> hotmail.com
> To: biopython-bugs <at> bioperl.org
> Subject: Blast bug

(Continue reading)

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