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biopython-bugs | 7 Nov 2002 15:52

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Message summary for PR#93
	From: andreas.kuntzagk <at> mdc-berlin.de
	Subject: GenBank-Format (Feature-Qualifier /motif)
	Date: Thu, 7 Nov 2002 09:52:51 -0500
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From andreas.kuntzagk <at> mdc-berlin.de Thu Nov  7 09:52:52 2002
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Date: Thu, 7 Nov 2002 09:52:51 -0500
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From: andreas.kuntzagk <at> mdc-berlin.de
To: biopython-bugs <at> bioperl.org
Subject: GenBank-Format (Feature-Qualifier /motif)

Full_Name: Andreas Kuntzagk
Module: genbank_format.py
Version: 
OS: 
Submission from: sulawesi.bioinf.mdc-berlin.de (141.80.80.60)

In Entry GI:4165449 (and others) there is a qualifier /motif in a CDS -Feature.
Currently the genbank_format.py doesn't allow this.

(Continue reading)

Thomas Sicheritz-Ponten | 8 Nov 2002 12:22

Picon

Picon

fast N-mer seach?

Hej,

What is the current best/fastest way to count all oligos of a given size
in a sequence? Is this something one could use mx.TextTools for? 
Or is it still faster to use the naive way by looping over i, extract all
seq[i:i+size] and increase the count in a dictionary ...?

What if I'd like to count all word/oligo frequencies up to size N?

stepping-into-the-optimization-swamp'ly y'rs
-thomas

--

-- 
Sicheritz-Ponten Thomas, Ph.D, thomas <at> biopython.org      (
Center for Biological Sequence Analysis                   \
BioCentrum-DTU, Technical University of Denmark            )
CBS: +45 45 252485      Building 208, DK-2800 Lyngby  ##----->
Fax: +45 45 931585      http://www.cbs.dtu.dk/thomas       )
                                                          /
     ... damn arrow eating trees ...                     (

biopython-bugs | 12 Nov 2002 09:58

Notification: incoming/94

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new message incoming/94

Message summary for PR#94
	From: hikokabu <at> hotmail.com
	Subject: GebBankParser
	Date: Tue, 12 Nov 2002 03:58:57 -0500
	0 replies 	0 followups

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

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From: hikokabu <at> hotmail.com
To: biopython-bugs <at> bioperl.org
Subject: GebBankParser

Full_Name: Hisahiko Sato
Module:  biopython-1.00a4.win32-py2.2.exe
Version:  biopython-1.00a4.win32-py2.2.exe
OS: win2000
Submission from: pvgw.m.chiba-u.ac.jp (133.82.145.42)

while parsing a GenBankFile I got stucked saying
""

(Continue reading)

biopython-bugs | 13 Nov 2002 01:52

Notification: incoming/95

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Message summary for PR#95
	From: Jeffrey Chang <jchang <at> smi.stanford.edu>
	Subject: Re: [Biopython-dev] Notification: incoming/94
	Date: Tue, 12 Nov 2002 16:50:53 -0800
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Subject: Re: [Biopython-dev] Notification: incoming/94
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(Continue reading)

Jeffrey Chang | 14 Nov 2002 00:09

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Re: Notification: incoming/93

Thanks!  I've applied the patch.

Jeff

On Thu, Nov 07, 2002 at 09:52:55AM -0500, biopython-bugs <at> bioperl.org wrote:
> JitterBug notification
> 
> new message incoming/93
> 
> Message summary for PR#93
> 	From: andreas.kuntzagk <at> mdc-berlin.de
> 	Subject: GenBank-Format (Feature-Qualifier /motif)
> 	Date: Thu, 7 Nov 2002 09:52:51 -0500
> 	0 replies 	0 followups
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
> >From andreas.kuntzagk <at> mdc-berlin.de Thu Nov  7 09:52:52 2002
> Received: from localhost (localhost [127.0.0.1])
> 	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gA7Eqp6J025565
> 	for <biopython-bugs <at> pw600a.bioperl.org>; Thu, 7 Nov 2002 09:52:52 -0500
> Date: Thu, 7 Nov 2002 09:52:51 -0500
> Message-Id: <200211071452.gA7Eqp6J025565 <at> pw600a.bioperl.org>
> From: andreas.kuntzagk <at> mdc-berlin.de
> To: biopython-bugs <at> bioperl.org
> Subject: GenBank-Format (Feature-Qualifier /motif)
> 
> Full_Name: Andreas Kuntzagk
> Module: genbank_format.py
> Version:

(Continue reading)

biopython-bugs | 14 Nov 2002 15:42

Notification: incoming/99

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Message summary for PR#99
	From: "hiko" <hikokabu <at> hotmail.com>
	Subject: Re: [Biopython-dev] Notification: incoming/94
	Date: Thu, 14 Nov 2002 23:43:06  0900
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biopython-bugs | 15 Nov 2002 07:32

Notification: incoming/100

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Message summary for PR#100
	From: Jeffrey Chang <jchang <at> SMI.Stanford.EDU>
	Subject: Re: [Biopython-dev] Notification: incoming/94
	Date: Thu, 14 Nov 2002 22:30:55 -0800
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To: hiko <hikokabu <at> hotmail.com>
Cc: biopython-bugs <at> bioperl.org
Subject: Re: [Biopython-dev] Notification: incoming/94
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Yves Bastide | 18 Nov 2002 23:15

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BioSQL and PostgreSQL

Hi,

I've adapted BioSQL/*.py to work with PostgreSQL.  Well, at least the 
tests pass... Patch attached, comments are welcome.

A few points:

* I've made utility classes for nonstandard SQL/DBAPI operations, e.g. 
retrieving the id of the last inserted record.  (The implementation is 
so-so, I know :).  There are Generic_dbutils, Mysql_dbutils and 
Pg_dbutils.  The choice is made according to the DBAPI module's name; 
only MySQLdb and psycopg are currently recognised.

* Replaced count = self.cursor.execute by self.cursor.execute and fetch

* Likewise, self.adaptor.execute_one("INSERT ...") --> 
self.adaptor.execute()

* SUBSTRING(biosequence_str, %s, %s) --> SUBSTRING(biosequence_str FROM 
%s FOR %s).  SQL is beautiful...

* I've modified test_BioSQL.py so that the first doesn't require a 
schema (it will DROP DATABASE/CREATE DATABASE like the other ones). I've 
also added tearDown()'s to close the database connections; otherwise, 
psycopg cannot drop the db.

* Modified open_database: psycopg uses a dsn, not keyword arguments.

(Done but not included in the patch: adaptations to the current 
biosql-schema CVS.)

(Continue reading)

biopython-bugs | 19 Nov 2002 04:25

Notification: incoming/101

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Message summary for PR#101
	From: "Thierry Vanhoudt" <sales <at> smoking.com.net>
	Subject: Discounted Tobacco
	Date: Mon, 18 Nov 2002 19:21:14  0100
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Dear Sir or Madam

(Continue reading)

biopython-bugs | 19 Nov 2002 04:25

Notification: incoming/102

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Message summary for PR#102
	From: "Thierry Vanhoudt" <sales <at> smoking.com.net>
	Subject: Discounted Smokes
	Date: Mon, 18 Nov 2002 19:21:14  0100
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