[Biopython-dev] Notification: incoming/78

[biopython-bugs at bioperl.org]

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
Content-Disposition: inline
User-Agent: Mutt/1.2.5.1i
In-Reply-To: <200208012113.g71LD6JD009195 at pw600a.bioperl.org>; from biopython-bugs at 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 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
> 
> 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 at biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev