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Thomas Hamelryck | 6 Feb 2003 20:09
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CVS problems?


Hi,

Is anything wrong with the biopython CVS server?
I keep getting "permission denied" when I try to checkout....

Regards,

-Thomas

---
Thomas Hamelryck
COMO-ULTR
Vrije Universiteit Brussel (VUB)
Belgium
http://homepages.vub.ac.be/~thamelry
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Jeffrey Chang | 6 Feb 2003 21:37
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Re: CVS problems?

It works for me.  However, we have changed the machine hosting the
read-write server to dev.open-bio.org.  Is that where you are trying
to checkout from?  If it still doesn't work, let me know.

Jeff

On Thu, Feb 06, 2003 at 08:09:38PM +0100, Thomas Hamelryck wrote:
> 
> Hi,
> 
> Is anything wrong with the biopython CVS server?
> I keep getting "permission denied" when I try to checkout....
> 
> Regards,
> 
> -Thomas
> 
> ---
> Thomas Hamelryck
> COMO-ULTR
> Vrije Universiteit Brussel (VUB)
> Belgium
> http://homepages.vub.ac.be/~thamelry
> 
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev <at> biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev
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Anthony Metzidis | 7 Feb 2003 09:43
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Possible Contribution: UCSC Blat and Ensembl SSAHA Sequence Locator

Hello,
We've developed a Python API for the UCSC 
BLAT(http://genome.ucsc.edu/cgi-bin/hgBlat?command=start) and Ensembl 
SSAHA (http://www.ensembl.org/Homo_sapiens/ssahaview) genome search tools.

Using our tool, you can input a series of dna sequences in Fasta format 
and then get the results back as dictionaries, indexed by the Fasta 
title, of dictionaries indexed by the fields presented by the web 
interfaces.

The http connection and parsing of the HTML results pages are handled by 
our tool.

We use these tools for locating large amounts of SNPs that are not yet 
annotated by the public DBs, or to relocate annotations that reference 
an older genome build to a newer one, for example.

We would like to contribute this to BioPython, if you think there would 
be an interest in it.

If so, could you offer advise about other existing BioPython interfaces 
that we should model ours after?  I would like the interface to be as 
consistent as possible with the rest of BioPython.

Any other advise on making contributions would be greatly appreciated.

Thanks,
Tony
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Jeffrey Chang | 7 Feb 2003 21:42
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Re: Possible Contribution: UCSC Blat and Ensembl SSAHA Sequence Locator

On Fri, Feb 07, 2003 at 10:43:29AM +0200, Anthony Metzidis wrote:
[I've reordered some paragraphs...]
> Hello,
> We've developed a Python API for the UCSC 
> BLAT(http://genome.ucsc.edu/cgi-bin/hgBlat?command=start) and Ensembl 
> SSAHA (http://www.ensembl.org/Homo_sapiens/ssahaview) genome search tools.

> We would like to contribute this to BioPython, if you think there would 
> be an interest in it.

Yes, there would definitely be interest in it!

> If so, could you offer advise about other existing BioPython interfaces 
> that we should model ours after?  I would like the interface to be as 
> consistent as possible with the rest of BioPython.

There's a few data types that should be supported.  More below...

> Using our tool, you can input a series of dna sequences in Fasta format 
> and then get the results back as dictionaries, indexed by the Fasta 
> title, of dictionaries indexed by the fields presented by the web 
> interfaces.

The DNA sequences should be Bio.Seq objects, and not require FASTA
format.  Also, the results should be in defined and documented objects
(for an example, see Bio.Blast.Record), rather than dictionaries.

> The http connection and parsing of the HTML results pages are handled by 
> our tool.
(Continue reading)

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Stefan Suhrer jun. | 10 Feb 2003 12:19
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README


You write in your README file that it is not required to install the Numerical 
Python 15.3
But after two hours of installation and compilation failures I can tell you 
that it is important to install it. Without it I could not compile biopython.

Please change this message in the README file and save the time of a lot of 
people

-----------------------------------------------------------------------------------------
Stefan Suhrer jun.
Stefan.Suhrer <at> came.sbg.ac.at

Institute of Chemistry and Biochemistry
University of Salzburg
C.A.M.E. - Center Of Applied Molecular Engineering
Jakob-Haringerstr. 3
A-5020 Salzburg
+43 - 662 - 8044-5796
-----------------------------------------------------------------------------------------
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Thomas Hamelryck | 10 Feb 2003 12:55
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Re: README

On Monday 10 February 2003 12:19 pm, Stefan Suhrer jun. wrote:
> You write in your README file that it is not required to install the
> Numerical Python 15.3
> But after two hours of installation and compilation failures I can tell you
> that it is important to install it. Without it I could not compile
> biopython.
>
> Please change this message in the README file and save the time of a lot of
> people

In fact, if you are using an RPM based linux system (as many people are), 
you need the pacakages Numpy AND Numpy-devel.

Greetings,

-Thomas

---
Thomas Hamelryck
COMO-ULTR
Vrije Universiteit Brussel (VUB)
Belgium
http://homepages.vub.ac.be/~thamelry
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Cayte | 12 Feb 2003 04:59

Artificial immune system

  I checked in a  new version with a pseudorandom generator as the default.

                       Cayte
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biopython-bugs | 12 Feb 2003 12:58

Notification: incoming/121

JitterBug notification

new message incoming/121

Message summary for PR#121
	From: gebauer-jung <at> ice.mpg.de
	Subject: typing mistakes
	Date: Wed, 12 Feb 2003 06:58:17 -0500
	0 replies 	0 followups

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

>From gebauer-jung <at> ice.mpg.de Wed Feb 12 06:58:18 2003
Received: from localhost (localhost [127.0.0.1])
	by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h1CBwH7E031348
	for <biopython-bugs <at> pw600a.bioperl.org>; Wed, 12 Feb 2003 06:58:17 -0500
Date: Wed, 12 Feb 2003 06:58:17 -0500
Message-Id: <200302121158.h1CBwH7E031348 <at> pw600a.bioperl.org>
From: gebauer-jung <at> ice.mpg.de
To: biopython-bugs <at> bioperl.org
Subject: typing mistakes
X-Spam-Status: No
X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang)

Full_Name: 
Module: Bio/Application/__init__.py and Bio/Blast/Applications.py
Version: biopython 1.10
OS: 
Submission from: n61.ice.mpg.de (141.5.20.61)
(Continue reading)

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biopython-bugs | 12 Feb 2003 12:58

Notification: incoming/122

JitterBug notification

new message incoming/122

Message summary for PR#122
	From: gebauer-jung <at> ice.mpg.de
	Subject: typing mistakes
	Date: Wed, 12 Feb 2003 06:58:30 -0500
	0 replies 	0 followups

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

>From gebauer-jung <at> ice.mpg.de Wed Feb 12 06:58:31 2003
Received: from localhost (localhost [127.0.0.1])
	by pw600a.bioperl.org (8.12.6/8.12.6) with ESMTP id h1CBwU7E031366
	for <biopython-bugs <at> pw600a.bioperl.org>; Wed, 12 Feb 2003 06:58:31 -0500
Date: Wed, 12 Feb 2003 06:58:30 -0500
Message-Id: <200302121158.h1CBwU7E031366 <at> pw600a.bioperl.org>
From: gebauer-jung <at> ice.mpg.de
To: biopython-bugs <at> bioperl.org
Subject: typing mistakes
X-Spam-Status: No
X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang)

Full_Name: 
Module: Bio/Application/__init__.py and Bio/Blast/Applications.py
Version: biopython 1.10
OS: 
Submission from: n61.ice.mpg.de (141.5.20.61)
(Continue reading)

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Jeffrey Chang | 12 Feb 2003 20:38
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Re: README

Thanks for the bug report!  I'll make the changes to the README file.
Do you have a complete list of the RPMs that have to be installed?

Jeff

On Mon, Feb 10, 2003 at 12:19:40PM +0100, Stefan Suhrer jun. wrote:
> 
> 
> You write in your README file that it is not required to install the Numerical 
> Python 15.3
> But after two hours of installation and compilation failures I can tell you 
> that it is important to install it. Without it I could not compile biopython.
> 
> Please change this message in the README file and save the time of a lot of 
> people
> 
> 
> 
> -----------------------------------------------------------------------------------------
> Stefan Suhrer jun.
> Stefan.Suhrer <at> came.sbg.ac.at
> 
> Institute of Chemistry and Biochemistry
> University of Salzburg
> C.A.M.E. - Center Of Applied Molecular Engineering
> Jakob-Haringerstr. 3
> A-5020 Salzburg
> +43 - 662 - 8044-5796
> -----------------------------------------------------------------------------------------
>
(Continue reading)

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Gmane