From biopython-bugs at bioperl.org  Thu Aug  1 17:13:06 2002
From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Notification: incoming/77
Message-ID: <200208012113.g71LD6JD009195@pw600a.bioperl.org>

JitterBug notification

new message incoming/77

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

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

>From zakano@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@pw600a.bioperl.org>; Thu, 1 Aug 2002 17:13:06 -0400
Date: Thu, 1 Aug 2002 17:13:06 -0400
Message-Id: <200208012113.g71LD6JD009191@pw600a.bioperl.org>
From: zakano@hotmail.com
To: biopython-bugs@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.

PROBLEM #1, IN:
    def _scan_database_info(self, uhandle, consumer):

THE FOLLOWING IS EXPECTED:
<b>Database:</b> All GenBank+EMBL+DDBJ+PDB sequences 
           1,357,022 sequences; 6,227,440,795 total letters

BLAST OUTPUT HAS BEEN CHANGED TO THE FOLLOWING:
<b>Database:</b> All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
GSS, or phase 0, 1 or 2 HTGS sequences) 
           1,357,022 sequences; 6,227,440,795 total letters

TO FIX THIS, I CHANGED THIS CODE:
        read_and_call(uhandle, consumer.database_info, contains='Database')
        read_and_call(uhandle, consumer.database_info, contains='sequences')
        read_and_call(uhandle, consumer.noevent, blank=1)

TO THIS CODE:
        read_and_call(uhandle, consumer.database_info, contains='Database')
        read_and_call(uhandle, consumer.database_info, contains='sequences')
        read_and_call(uhandle, consumer.database_info, contains='total')
        read_and_call(uhandle, consumer.noevent, blank=1)


PROBLEM #2, IN:
    def _scan_database_report(self, uhandle, consumer):

THE FOLLOWING IS EXPECTED:
<PRE>
   Database: Non-redundant SwissProt sequences
     Posted date:  Dec 18, 1999  8:26 PM

BLAST OUTPUT HAS BEEN CHANGED TO THE FOLLOWING:
<PRE>
  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
  or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Aug 1, 2002 12:00 AM

TO FIX THIS, I CHANGED THIS CODE:
        read_and_call(uhandle, consumer.noevent, start='<PRE>')
        read_and_call(uhandle, consumer.noevent, start='  Database')
        read_and_call(uhandle, consumer.posted_date, start='    Posted')

TO THIS CODE:
        read_and_call(uhandle, consumer.noevent, start='<PRE>')
        read_and_call(uhandle, consumer.noevent, start='  Database')
        read_and_call(uhandle, consumer.database, start='  or')
        read_and_call(uhandle, consumer.posted_date, start='    Posted')






From jchang at smi.stanford.edu  Thu Aug  1 22:39:26 2002
From: jchang at smi.stanford.edu (Jeffrey Chang)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] The signal module on the Mac
In-Reply-To: <B96D7E2D.168D%Y.Benita@pharm.uu.nl>; from Y.Benita@pharm.uu.nl on Wed, Jul 31, 2002 at 11:44:45AM +0200
References: <B96D7E2D.168D%Y.Benita@pharm.uu.nl>
Message-ID: <20020801193926.B88356@springfield.stanford.edu>

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
> -- 
> Yair Benita
> Pharmaceutical Proteomics
> Utrecht University
> 
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

From Y.Benita at pharm.uu.nl  Fri Aug  2 05:24:50 2002
From: Y.Benita at pharm.uu.nl (Yair Benita)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] New BioPython for MacPython Carbon
Message-ID: <B9701C82.16BE%Y.Benita@pharm.uu.nl>

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


From biopython-bugs at bioperl.org  Sun Aug  4 13:26:50 2002
From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Notification: incoming/78
Message-ID: <200208041726.g74HQoJD007485@pw600a.bioperl.org>

JitterBug notification

new message incoming/78

Message summary for PR#78
	From: Jeffrey Chang <jchang@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@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@bioperl.org>; Sun, 4 Aug 2002 13:26:49 -0400
Received: (from jchang@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@smi.stanford.edu>
To: zakano@hotmail.com
Cc: biopython-bugs@bioperl.org
Subject: Re: [Biopython-dev] Notification: incoming/77
Message-ID: <20020804102328.B96551@springfield.stanford.edu>
Mail-Followup-To: zakano@hotmail.com, biopython-bugs@bioperl.org
References: <200208012113.g71LD6JD009195@pw600a.bioperl.org>
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Content-Type: text/plain; charset=us-ascii
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In-Reply-To: <200208012113.g71LD6JD009195@pw600a.bioperl.org>; from biopython-bugs@bioperl.org on Thu, Aug 01, 2002 at 05:13:06PM -0400

Thanks for the bug report and patch.  We are at BOSC/ISMB this week,
and will get to this afterwards.

Jeff

On Thu, Aug 01, 2002 at 05:13:06PM -0400, biopython-bugs@bioperl.org wrote:
> JitterBug notification
> 
> new message incoming/77
> 
> Message summary for PR#77
> 	From: zakano@hotmail.com
> 	Subject: Blast bug
> 	Date: Thu, 1 Aug 2002 17:13:06 -0400
> 	0 replies 	0 followups
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
> >From zakano@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@pw600a.bioperl.org>; Thu, 1 Aug 2002 17:13:06 -0400
> Date: Thu, 1 Aug 2002 17:13:06 -0400
> Message-Id: <200208012113.g71LD6JD009191@pw600a.bioperl.org>
> From: zakano@hotmail.com
> To: biopython-bugs@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.
> 
> PROBLEM #1, IN:
>     def _scan_database_info(self, uhandle, consumer):
> 
> THE FOLLOWING IS EXPECTED:
> <b>Database:</b> All GenBank+EMBL+DDBJ+PDB sequences 
>            1,357,022 sequences; 6,227,440,795 total letters
> 
> BLAST OUTPUT HAS BEEN CHANGED TO THE FOLLOWING:
> <b>Database:</b> All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
> GSS, or phase 0, 1 or 2 HTGS sequences) 
>            1,357,022 sequences; 6,227,440,795 total letters
> 
> TO FIX THIS, I CHANGED THIS CODE:
>         read_and_call(uhandle, consumer.database_info, contains='Database')
>         read_and_call(uhandle, consumer.database_info, contains='sequences')
>         read_and_call(uhandle, consumer.noevent, blank=1)
> 
> TO THIS CODE:
>         read_and_call(uhandle, consumer.database_info, contains='Database')
>         read_and_call(uhandle, consumer.database_info, contains='sequences')
>         read_and_call(uhandle, consumer.database_info, contains='total')
>         read_and_call(uhandle, consumer.noevent, blank=1)
> 
> 
> PROBLEM #2, IN:
>     def _scan_database_report(self, uhandle, consumer):
> 
> THE FOLLOWING IS EXPECTED:
> <PRE>
>    Database: Non-redundant SwissProt sequences
>      Posted date:  Dec 18, 1999  8:26 PM
> 
> BLAST OUTPUT HAS BEEN CHANGED TO THE FOLLOWING:
> <PRE>
>   Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
>   or phase 0, 1 or 2 HTGS sequences)
>     Posted date:  Aug 1, 2002 12:00 AM
> 
> TO FIX THIS, I CHANGED THIS CODE:
>         read_and_call(uhandle, consumer.noevent, start='<PRE>')
>         read_and_call(uhandle, consumer.noevent, start='  Database')
>         read_and_call(uhandle, consumer.posted_date, start='    Posted')
> 
> TO THIS CODE:
>         read_and_call(uhandle, consumer.noevent, start='<PRE>')
>         read_and_call(uhandle, consumer.noevent, start='  Database')
>         read_and_call(uhandle, consumer.database, start='  or')
>         read_and_call(uhandle, consumer.posted_date, start='    Posted')
> 
> 
> 
> 
> 
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev



From biopython-bugs at bioperl.org  Mon Aug  5 08:16:43 2002
From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Notification: incoming/79
Message-ID: <200208051216.g75CGhJD015186@pw600a.bioperl.org>

JitterBug notification

new message incoming/79

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

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

>From pears78pretty@hotmail.com Mon Aug  5 08:16:41 2002
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Reply-To: pears78pretty@hotmail.com
From: 宏府飘聪 <pears78pretty@hotmail.com>
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From biopython-bugs at bioperl.org  Mon Aug  5 20:38:24 2002
From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Notification: incoming/80
Message-ID: <200208060038.g760cOJD019975@pw600a.bioperl.org>

JitterBug notification

new message incoming/80

Message summary for PR#80
	From: daishi@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@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@pw600a.bioperl.org>; Mon, 5 Aug 2002 20:38:23 -0400
Date: Mon, 5 Aug 2002 20:38:23 -0400
Message-Id: <200208060038.g760cNJD019971@pw600a.bioperl.org>
From: daishi@egcrc.net
To: biopython-bugs@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:

        if self._parser.data:
            str = self._parser.data
        elif is_newline:
            str = '\n'
        return str

There needs to be a final else clause to
catch the circumstance when the file ends
with a tag but no newline. As it is currently,
such a tag will be returned by SGMLStripper
since str would not be redefined.

Since this can only occur at the end of a file,
I believe this can just be changed to:

        if self._parser.data:
            str = self._parser.data
        elif is_newline:
            str = '\n'
        else:
            str = ''
        return str





From jchang at smi.stanford.edu  Tue Aug  6 12:42:51 2002
From: jchang at smi.stanford.edu (Jeffrey Chang)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Biopython: The Flattening
Message-ID: <20020806094251.A1694@springfield.stanford.edu>

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

From biopython-bugs at bioperl.org  Tue Aug  6 13:46:05 2002
From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Notification: incoming/81
Message-ID: <200208061746.g76Hk5JD028572@pw600a.bioperl.org>

JitterBug notification

new message incoming/81

Message summary for PR#81
	From: Jeffrey Chang <jchang@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@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@bioperl.org>; Tue, 6 Aug 2002 13:46:04 -0400
Received: (from jchang@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@smi.stanford.edu>
To: daishi@egcrc.net
Cc: biopython-bugs@bioperl.org
Subject: Re: [Biopython-dev] Notification: incoming/80
Message-ID: <20020806104233.B1810@springfield.stanford.edu>
Mail-Followup-To: daishi@egcrc.net, biopython-bugs@bioperl.org
References: <200208060038.g760cOJD019975@pw600a.bioperl.org>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
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In-Reply-To: <200208060038.g760cOJD019975@pw600a.bioperl.org>; from biopython-bugs@bioperl.org on Mon, Aug 05, 2002 at 08:38:24PM -0400

Hi Daishi,

Thanks for the report and patch.  I am at ISMB right now.  I will look
at this when I get back home at the end of this week.

Jeff


On Mon, Aug 05, 2002 at 08:38:24PM -0400, biopython-bugs@bioperl.org wrote:
> JitterBug notification
> 
> new message incoming/80
> 
> Message summary for PR#80
> 	From: daishi@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@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@pw600a.bioperl.org>; Mon, 5 Aug 2002 20:38:23 -0400
> Date: Mon, 5 Aug 2002 20:38:23 -0400
> Message-Id: <200208060038.g760cNJD019971@pw600a.bioperl.org>
> From: daishi@egcrc.net
> To: biopython-bugs@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:
> 
>         if self._parser.data:
>             str = self._parser.data
>         elif is_newline:
>             str = '\n'
>         return str
> 
> There needs to be a final else clause to
> catch the circumstance when the file ends
> with a tag but no newline. As it is currently,
> such a tag will be returned by SGMLStripper
> since str would not be redefined.
> 
> Since this can only occur at the end of a file,
> I believe this can just be changed to:
> 
>         if self._parser.data:
>             str = self._parser.data
>         elif is_newline:
>             str = '\n'
>         else:
>             str = ''
>         return str
> 
> 
> 
> 
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev



From jchang at smi.stanford.edu  Tue Aug  6 14:53:45 2002
From: jchang at smi.stanford.edu (Jeffrey Chang)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Notification: incoming/80
In-Reply-To: <200208060038.g760cOJD019975@pw600a.bioperl.org>; from biopython-bugs@bioperl.org on Mon, Aug 05, 2002 at 08:38:24PM -0400
References: <200208060038.g760cOJD019975@pw600a.bioperl.org>
Message-ID: <20020806115345.C2017@springfield.stanford.edu>

I have committed this.  Thanks!

Jeff

On Mon, Aug 05, 2002 at 08:38:24PM -0400, biopython-bugs@bioperl.org wrote:
> JitterBug notification
> 
> new message incoming/80
> 
> Message summary for PR#80
> 	From: daishi@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@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@pw600a.bioperl.org>; Mon, 5 Aug 2002 20:38:23 -0400
> Date: Mon, 5 Aug 2002 20:38:23 -0400
> Message-Id: <200208060038.g760cNJD019971@pw600a.bioperl.org>
> From: daishi@egcrc.net
> To: biopython-bugs@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:
> 
>         if self._parser.data:
>             str = self._parser.data
>         elif is_newline:
>             str = '\n'
>         return str
> 
> There needs to be a final else clause to
> catch the circumstance when the file ends
> with a tag but no newline. As it is currently,
> such a tag will be returned by SGMLStripper
> since str would not be redefined.
> 
> Since this can only occur at the end of a file,
> I believe this can just be changed to:
> 
>         if self._parser.data:
>             str = self._parser.data
>         elif is_newline:
>             str = '\n'
>         else:
>             str = ''
>         return str
> 
> 
> 
> 
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

From jchang at smi.stanford.edu  Tue Aug  6 15:03:02 2002
From: jchang at smi.stanford.edu (Jeffrey Chang)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Notification: incoming/77
In-Reply-To: <200208012113.g71LD6JD009195@pw600a.bioperl.org>; from biopython-bugs@bioperl.org on Thu, Aug 01, 2002 at 05:13:06PM -0400
References: <200208012113.g71LD6JD009195@pw600a.bioperl.org>
Message-ID: <20020806120301.D2017@springfield.stanford.edu>

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@bioperl.org wrote:
> JitterBug notification
> 
> new message incoming/77
> 
> Message summary for PR#77
> 	From: zakano@hotmail.com
> 	Subject: Blast bug
> 	Date: Thu, 1 Aug 2002 17:13:06 -0400
> 	0 replies 	0 followups
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
> >From zakano@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@pw600a.bioperl.org>; Thu, 1 Aug 2002 17:13:06 -0400
> Date: Thu, 1 Aug 2002 17:13:06 -0400
> Message-Id: <200208012113.g71LD6JD009191@pw600a.bioperl.org>
> From: zakano@hotmail.com
> To: biopython-bugs@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.
> 
> PROBLEM #1, IN:
>     def _scan_database_info(self, uhandle, consumer):
> 
> THE FOLLOWING IS EXPECTED:
> <b>Database:</b> All GenBank+EMBL+DDBJ+PDB sequences 
>            1,357,022 sequences; 6,227,440,795 total letters
> 
> BLAST OUTPUT HAS BEEN CHANGED TO THE FOLLOWING:
> <b>Database:</b> All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
> GSS, or phase 0, 1 or 2 HTGS sequences) 
>            1,357,022 sequences; 6,227,440,795 total letters
> 
> TO FIX THIS, I CHANGED THIS CODE:
>         read_and_call(uhandle, consumer.database_info, contains='Database')
>         read_and_call(uhandle, consumer.database_info, contains='sequences')
>         read_and_call(uhandle, consumer.noevent, blank=1)
> 
> TO THIS CODE:
>         read_and_call(uhandle, consumer.database_info, contains='Database')
>         read_and_call(uhandle, consumer.database_info, contains='sequences')
>         read_and_call(uhandle, consumer.database_info, contains='total')
>         read_and_call(uhandle, consumer.noevent, blank=1)
> 
> 
> PROBLEM #2, IN:
>     def _scan_database_report(self, uhandle, consumer):
> 
> THE FOLLOWING IS EXPECTED:
> <PRE>
>    Database: Non-redundant SwissProt sequences
>      Posted date:  Dec 18, 1999  8:26 PM
> 
> BLAST OUTPUT HAS BEEN CHANGED TO THE FOLLOWING:
> <PRE>
>   Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
>   or phase 0, 1 or 2 HTGS sequences)
>     Posted date:  Aug 1, 2002 12:00 AM
> 
> TO FIX THIS, I CHANGED THIS CODE:
>         read_and_call(uhandle, consumer.noevent, start='<PRE>')
>         read_and_call(uhandle, consumer.noevent, start='  Database')
>         read_and_call(uhandle, consumer.posted_date, start='    Posted')
> 
> TO THIS CODE:
>         read_and_call(uhandle, consumer.noevent, start='<PRE>')
>         read_and_call(uhandle, consumer.noevent, start='  Database')
>         read_and_call(uhandle, consumer.database, start='  or')
>         read_and_call(uhandle, consumer.posted_date, start='    Posted')
> 
> 
> 
> 
> 
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

From dyoo at acoma.Stanford.EDU  Wed Aug  7 16:46:45 2002
From: dyoo at acoma.Stanford.EDU (Danny Yoo)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Strange Genbank feature description: how should biopython handle
 this?
Message-ID: <Pine.GSO.4.44.0208071256550.23563-100000@acoma.Stanford.EDU>

Hi everyone,


Ok, I fiddling around with the Genbank parser.  In one of my test cases,
there's one particular entry that's very evil.  It comes from AP000423
(GI:5881673), as gene RPS12:

     gene            join(complement(98562..98793),complement(97999..98024),
                     complement(69611..69724),139856..140087,140625..140650)
                     /gene="rps12"




Here's how Biopython is initializing this feature as:

###
type: gene
location: (98561..140650)
ref: None:None
strand: None
qualifiers:
	Key: gene, Value: ['rps12']
Sub-Features
type: gene
location: (98561..98793)
ref: None:None
strand: -1
qualifiers:

type: gene
location: (97998..98024)
ref: None:None
strand: -1
qualifiers:

type: gene
location: (69610..69724)
ref: None:None
strand: -1
qualifiers:

type: gene
location: (139855..140087)
ref: None:None
strand: None
qualifiers:

type: gene
location: (140624..140650)
ref: None:None
strand: None
qualifiers:
###


The LocationParser itself appears to be doing it's job, as I see that:

###
Function('join', [Function('complement', [AbsoluteLocation(None,
Range(Integer(98562), Integer(98793)))]), Function('complement',
[AbsoluteLocation(None, Range(Integer(97999), Integer(98024)))]),
Function('complement', [AbsoluteLocation(None, Range(Integer(69611),
Integer(69724)))]), AbsoluteLocation(None, Range(Integer(139856),
Integer(140087))), AbsoluteLocation(None, Range(Integer(140625),
Integer(140650)))])
###



Having a strand of 'None' doesn't appear to be right.  I've been staring
at 'Bio.GenBank.__init__.py' for a while, and it appears that the default
value for the strand isn't set unless the self._seq_type is equal to
"DNA".  I don't quite understand all of the code yet, but the following
change appears to fix this particular case:


Index: Bio/GenBank/__init__.py
===================================================================
RCS file: /home/repository/biopython/biopython/Bio/GenBank/__init__.py,v
retrieving revision 1.29
diff -u -r1.29 __init__.py
--- Bio/GenBank/__init__.py	2002/04/16 15:45:26	1.29
+++ Bio/GenBank/__init__.py	2002/08/07 20:43:28
@@ -636,8 +636,9 @@

         # assume positive strand to start with if we have DNA. The
         # complement in the location will change this later.
-        if self._seq_type == "DNA":
-            self._cur_feature.strand = 1
+##         if self._seq_type == "DNA":
+##             self._cur_feature.strand = 1
+        self._cur_feature.strand = 1

     def location(self, content):
         """Parse out location information from the location string.
@@ -735,7 +736,7 @@
             new_sub_feature.ref = cur_feature.ref
             new_sub_feature.ref_db = cur_feature.ref_db
             new_sub_feature.strand = cur_feature.strand
-
+            assert(new_sub_feature.strand in (1, -1)) ## debug
             # set the information for the inner element
             self._set_location_info(inner_element, new_sub_feature)



What's the right way of fixing this problem?  Thank you!


From katel at worldpath.net  Thu Aug  8 04:14:45 2002
From: katel at worldpath.net (Cayte)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] LocusLink
Message-ID: <014901c23eb3$a8ef0520$569403cf@pcklindner>

I added a parser for the LocusLink flat file.  Next I plan to hook in Mindy,
provide a UniGene flat file parser.  I also plan to make the Ais parameters
configurable so I can do experiments.

                                         Cayte


From jhessel at mail.utexas.edu  Thu Aug  8 09:42:31 2002
From: jhessel at mail.utexas.edu (Jay Hesselberth)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] genbank_format.py patch
Message-ID: <1028814152.5618.2.camel@io.icmb.utexas.edu>

I've got a patch for genbank_format.py; the feature key 'snoRNA' was not
included.

<snip>
*** genbank_format.py.orig  Thu Aug  8 08:36:05 2002
--- genbank_format.py   Thu Aug  8 08:36:43 2002
***************
*** 404,410 ****
      "5'clip",           # 5'-most region of a precursor transcript
removed'
                          # in processing
      "5'UTR",            # 5' untranslated region (leader)'
!     "-"                 # (hyphen)      Placeholder
  )
  valid_feature_keys = map(Martel.Str, feature_key_names)
  
--- 404,411 ----
      "5'clip",           # 5'-most region of a precursor transcript
removed'
                          # in processing
      "5'UTR",            # 5' untranslated region (leader)'
!     "-",                # (hyphen)      Placeholder
!     "snoRNA"            # small nucleolar RNA
  )
  valid_feature_keys = map(Martel.Str, feature_key_names)
  
</snip>

Jay

-- 
________________________________________________
Jay Hesselberth          jhessel@mail.utexas.edu

University of Texas      (512) 471-6445
2500 Speedway / A4800
Austin, TX  78712


From katel at worldpath.net  Fri Aug  9 16:30:59 2002
From: katel at worldpath.net (Katharine Lindner)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Genbank Dictionary
Message-ID: <3D542683.3010708@worldpath.net>

 I  was thinking of providing a Dictionary interface to LocusLink.  I 
don't see anything specific to GenBank in the class.  For this reason I 
suggest adding it to Index or where it will be available to other 
parsers w/o duplication.

                                              Cayte


From jchang at smi.stanford.edu  Sun Aug 11 01:16:19 2002
From: jchang at smi.stanford.edu (Jeffrey Chang)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] moved some packages around
Message-ID: <20020810221619.A16863@springfield.stanford.edu>

Hello everybody,

I've moved some packages around to make them more visible to end
users.  Most significantly, the Bio/Tools/ directory is now gone.
Everything in there has been moved up one level.  There are also a few
other minor changes.

I believe I have fixed all the references to the moved files.
However, please be on the lookout for import errors, and let me know
if I've missed something.

Thanks!
Jeff

P.S.  for your next checkout, be sure to do:
cvs update -P -d

From chapmanb at arches.uga.edu  Mon Aug 12 11:56:45 2002
From: chapmanb at arches.uga.edu (Brad Chapman)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Strange Genbank feature description: how should biopython handle this?
In-Reply-To: <Pine.GSO.4.44.0208071256550.23563-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0208071256550.23563-100000@acoma.Stanford.EDU>
Message-ID: <20020812155645.GC43844@ci350185-a.athen1.ga.home.com>

Hi Danny;
Sorry to be so slow in getting back with you. Evil post-conference
mounds of work piled up on me.

> Ok, I fiddling around with the Genbank parser.  In one of my test cases,
> there's one particular entry that's very evil.  It comes from AP000423
> (GI:5881673), as gene RPS12:
[...]
> Having a strand of 'None' doesn't appear to be right.  

Yes, actually I ran into this problem right before the conference with
Jeremy and thought I had committed the fix (ugh, forgot. Bad Brad!
Bad!). The problem is that the following code:

> -        if self._seq_type == "DNA":
> -            self._cur_feature.strand = 1

only will set the strand if we are dealing with a DNA molecule. The
problem is that your _seq_type looks like:

DNA     circular

which mucks things up badly. I've changed this code so it looks like:

if self._seq_type.find("DNA") >= 0:

so that we only require DNA to be in the name. I think this will fix
this and the changes are in CVS. Please let me know if this doesn't
help.

> +            assert(new_sub_feature.strand in (1, -1)) ## debug

Things aren't actually quite as easy to debug as this. The strand in
Biopython can take on 4 values:

None --> protein and RNA, which don't have any strand information
1 --> DNA on the plus strand
-1 --> DNA on the minus strand
0 --> DNA on both strands

Hopefully this explains things and fixes your problem. If not, feel free
to drop another e-mail!
Brad

From chapmanb at arches.uga.edu  Mon Aug 12 12:04:17 2002
From: chapmanb at arches.uga.edu (Brad Chapman)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] genbank_format.py patch
In-Reply-To: <1028814152.5618.2.camel@io.icmb.utexas.edu>
References: <1028814152.5618.2.camel@io.icmb.utexas.edu>
Message-ID: <20020812160417.GD43844@ci350185-a.athen1.ga.home.com>

Hey Jay;

> I've got a patch for genbank_format.py; the feature key 'snoRNA' was not
> included.
[...]

Thanks, I've fixed it in CVS. Aaah, those sneaky feature keys; new ones
keep sneaking up all the time!

Brad

From biopython-bugs at bioperl.org  Fri Aug 16 06:50:43 2002
From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Notification: incoming/82
Message-ID: <200208161050.g7GAohJD013471@pw600a.bioperl.org>

JitterBug notification

new message incoming/82

Message summary for PR#82
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	Subject: ............................
	Date: Wed,16 .... 2002 18:50:54  0800
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From lcoillio at pharma-etu.univ-lille2.fr  Mon Aug 19 12:29:11 2002
From: lcoillio at pharma-etu.univ-lille2.fr (louis_coilliot)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] bug: swissprot record parser errors
Message-ID: <102977455130889-19182930889lcoillio@pharma-etu.univ-lille2.fr>

This little program:



#!/usr/bin/env python
# reading a SwissProt entry from a file

from Bio.SwissProt import SProt
from sys import *

try:
    handle = open(argv[1])
    sp = SProt.Iterator(handle, SProt.RecordParser())
    record = sp.next()
    print record.entry_name
    print
except:
    print "error"



doesn't work with some records, for example:
http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?O75398
http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?P41964

I don't know why. Any idea ?
                             


From jchang at smi.stanford.edu  Mon Aug 19 13:43:26 2002
From: jchang at smi.stanford.edu (Jeffrey Chang)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] bug: swissprot record parser errors
In-Reply-To: <102977455130889-19182930889lcoillio@pharma-etu.univ-lille2.fr>; from lcoillio@pharma-etu.univ-lille2.fr on Mon, Aug 19, 2002 at 04:29:11PM +0000
References: <102977455130889-19182930889lcoillio@pharma-etu.univ-lille2.fr>
Message-ID: <20020819104325.A40615@springfield.stanford.edu>

Are you using the updated SProt module from the CVS?  The format's
changed a bit since the last release of biopython, and some problems
have been fixed since then.

Jeff


On Mon, Aug 19, 2002 at 04:29:11PM +0000, louis_coilliot wrote:
> This little program:
> 
> 
> 
> #!/usr/bin/env python
> # reading a SwissProt entry from a file
> 
> from Bio.SwissProt import SProt
> from sys import *
> 
> try:
>     handle = open(argv[1])
>     sp = SProt.Iterator(handle, SProt.RecordParser())
>     record = sp.next()
>     print record.entry_name
>     print
> except:
>     print "error"
> 
> 
> 
> doesn't work with some records, for example:
> http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?O75398
> http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?P41964
> 
> I don't know why. Any idea ?
>                              
> 
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

From dyoo at hkn.eecs.berkeley.edu  Mon Aug 19 14:08:54 2002
From: dyoo at hkn.eecs.berkeley.edu (Danny Yoo)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] bug: swissprot record parser errors
In-Reply-To: <102977455130889-19182930889lcoillio@pharma-etu.univ-lille2.fr>
Message-ID: <Pine.LNX.4.44.0208191039320.9072-100000@hkn.eecs.berkeley.edu>


On Mon, 19 Aug 2002, louis_coilliot wrote:

> This little program:
>
>
>
> #!/usr/bin/env python
> # reading a SwissProt entry from a file
>
> from Bio.SwissProt import SProt
> from sys import *
>
> try:
>     handle = open(argv[1])
>     sp = SProt.Iterator(handle, SProt.RecordParser())
>     record = sp.next()
>     print record.entry_name
>     print
> except:
>     print "error"
>
>
>
> doesn't work with some records, for example:
> http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?O75398
> http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?P41964
>
> I don't know why. Any idea ?


I see the following error message when trying your test program on
075398, using BioPython 1.0:


###
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/tmp/python-26514l6q", line 10, in getRecordName
  File
"/opt/Python-2.1.1/lib/python2.1/site-packages/Bio/SwissProt/SProt.py",
line 168, in next
    return self._parser.parse(File.StringHandle(data))
  File
"/opt/Python-2.1.1/lib/python2.1/site-packages/Bio/SwissProt/SProt.py",
line 289, in parse
    self._scanner.feed(handle, self._consumer)
  File
"/opt/Python-2.1.1/lib/python2.1/site-packages/Bio/SwissProt/SProt.py",
line 332, in feed
    self._scan_record(uhandle, consumer)
  File
"/opt/Python-2.1.1/lib/python2.1/site-packages/Bio/SwissProt/SProt.py",
line 337, in _scan_record
    fn(self, uhandle, consumer)
  File
"/opt/Python-2.1.1/lib/python2.1/site-packages/Bio/SwissProt/SProt.py",
line 411, in _scan_reference
    self._scan_ra(uhandle, consumer)
  File
"/opt/Python-2.1.1/lib/python2.1/site-packages/Bio/SwissProt/SProt.py",
line 433, in _scan_ra
    one_or_more=1)
  File
"/opt/Python-2.1.1/lib/python2.1/site-packages/Bio/SwissProt/SProt.py",
line 359, in _scan_line
    read_and_call(uhandle, event_fn, start=line_type)
  File
"/opt/Python-2.1.1/lib/python2.1/site-packages/Bio/ParserSupport.py", line
326, in read_and_call
    raise SyntaxError, errmsg
SyntaxError: Line does not start with 'RA':
RP   LYS-304.
###


Record 075398 has two RP lines in it's first reference:

###
RN   [1]
RP   SEQUENCE FROM N.A. (ISOFORMS 1 AND 3), AND MUTAGENESIS OF ARG-302 AND
RP   LYS-304.
###

I'm staring at SProt.py's parser now to see how it handles consecutive
RP's.  Hmmm.... ah!


This problem has been fixed in CVS already.  Before, the parser tried
scanning RP's like this:


### Biopython 1.0,
    def _scan_rp(self, uhandle, consumer):
        self._scan_line('RP', uhandle, consumer.reference_position,
                        exactly_one=1)
###



but in CVS, this has been corrected to:

### Biopython CVS
    def _scan_rp(self, uhandle, consumer):
        self._scan_line('RP', uhandle, consumer.reference_position,
                        one_or_more=1)
###

to account for multiple RP lines.  Try checking BioPython out from CVS:
your program should work then.



Good luck to you!


From biopython-bugs at bioperl.org  Wed Aug 21 04:19:48 2002
From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Notification: incoming/83
Message-ID: <200208210819.g7L8JmIn007794@pw600a.bioperl.org>

JitterBug notification

new message incoming/83

Message summary for PR#83
	From: wart@tepkom.ru
	Subject: sequtils.py gives warning under Python 2.2
	Date: Wed, 21 Aug 2002 04:19:47 -0400
	0 replies 	0 followups

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

>From wart@tepkom.ru Wed Aug 21 04:19:47 2002
Received: from localhost (localhost [127.0.0.1])
	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g7L8JlIn007790
	for <biopython-bugs@pw600a.bioperl.org>; Wed, 21 Aug 2002 04:19:47 -0400
Date: Wed, 21 Aug 2002 04:19:47 -0400
Message-Id: <200208210819.g7L8JlIn007790@pw600a.bioperl.org>
From: wart@tepkom.ru
To: biopython-bugs@bioperl.org
Subject: sequtils.py gives warning under Python 2.2

Full_Name: Wartan Hachaturow
Module: Bio/sequtils.py
Version: 1.00a4
OS: Debian GNU/Linux
Submission from: local.eye.spbu.ru (195.19.226.65)


sequtils.py:208: SyntaxWarning: import * only allowed at module level
  def xGC_skew(seq, window = 1000, zoom = 100,

This only happens under python 2.2.
The patch is simple ;)

--- ./sequtils.py.orig  2002-08-21 12:18:11.000000000 +0400
+++ ./sequtils.py       2002-08-21 12:18:24.000000000 +0400
@@ -209,7 +209,7 @@
                          r = 300, px = 100, py = 100):
    " calculates and plots normal and accumulated GC skew (GRAPHICS !!!) "
    
-   from Tkinter import *
+   from Tkinter import Scrollbar, Canvas
    from math import pi, sin, cos, log
 
    yscroll = Scrollbar(orient = VERTICAL)



From wart at tepkom.ru  Wed Aug 21 04:35:22 2002
From: wart at tepkom.ru (Wartan Hachaturow)
Date: Sat Mar  5 14:43:15 2005
Subject: [Biopython-dev] Biopython's Debian packages.
Message-ID: <20020821083521.GA18705@mojo.tepkom.ru>

Hello.

I've packaged the 1.00a4 release of Biopython into Debian packages.
Hope they would get it into Debian after testing.
Packages are available at
http://people.debian.org/~wart/biopython/

-- 
Regards, Wartan.
"Computers are not intelligent. They only think they are."