bugzilla-daemon | 3 Apr 13:30 2005

[Bug 1767] New: Bio/trie.c can crash on Windows

http://bugzilla.open-bio.org/show_bug.cgi?id=1767

           Summary: Bio/trie.c can crash on Windows
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Windows 2000
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: mdehoon <at> ims.u-tokyo.ac.jp

In Bio/trie.c, the function strdup is being used, which is not part of the
ANSI-C standard. As a result, when Bio/trie.c is compiled, the resulting trie
module links to two C runtime libraries (mscvrt.dll and mscvr71.dll), which are
incompatible with each other and can cause crashes. To fix this bug, we need to
write our own strdup function using ANSI-C standard functions.

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Re:

To post to biopython-dev <at> biopython.org, you need to subscribe first via the 
biopython website. This was done to stop the huge amounts of spam we were 
receiving earlier. If you want to submit a patch, the best way is to create a 
bug report first (also via the biopython website) and then add an attachment 
containing the patch. Patches sent to the mailing list tend to get lost, and are 
sometimes rejected by the spam filter. If you want to submit a larger piece of 
code, for example a new module, you can post a message to 
biopython-dev <at> biopython.org first to describe the code, and then send it to one 
of the developers.

Hope this helps!

--Michiel.

Glen van Ginkel wrote:

> I tried to submit code to biopython-dev <at> biopython.org but got a message
> telling me I was not allowed to mail them
> 
>  
> 
> How do I go about submitting code?
> 
>  
> 
> Thankyou
> 
>  
> 
> Glen van Ginkel
(Continue reading)

Glen van Ginkel | 7 Apr 09:13 2005
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Hmmer integration modules/package

Hi Guys

As a project for my MRes in bioinformatics I have had to write a Python 
package that would expand Biopythons capabilities in interacting with useful 
programs. Here I submit code to interact with the Hmmer suite of programs. 

Basically, you instantiate the Hmmer object (Like a Hmmer commandline builder 
object), build a commandline, execute it and grab the results. Really simple 
for the user. This only works in UNIX since Hmmer is not available on Windows 
platforms and it obviously assumes you have Hmmer already installed on your 
PC. 
I have also tried to integrate the Bio.Align.Generic alignment object sothat 
the Hmmer object is able to handle alignment objects by writing the records 
of the alignment object to a temporary fasta file. 

Since I have to write this up as a report I would greatly appreciate any 
criticism of any kind and perhaps some suggestions as to how I might improve 
the code. Also, If you can think of any other ways to implement the Hmmer 
stuff please let me know. 

At the moment I am working on a test suite for the project. If you would like 
the code I have written to exercise some of the methods please let me know 
and I'll send it over. 
I also have a bit of documentation I would like to add to the Application 
package because I feel if failed to help me concerning certain aspects. How 
would I go about this?

I look forward to hearing your suggestions. 

Glen van Ginkel
(Continue reading)

Glen van Ginkel | 7 Apr 14:10 2005
Picon

Hmmer integration modules/package

Hi Guys

As a project for my MRes in bioinformatics I have had to write a Python 
package that would expand Biopythons capabilities in interacting with useful 
programs. Here I submit code to interact with the Hmmer suite of programs. 

Basically, you instantiate the Hmmer object (Like a Hmmer commandline builder 
object), build a commandline, execute it and grab the results. Really simple 
for the user. This only works in UNIX since Hmmer is not available on Windows 
platforms and it obviously assumes you have Hmmer already installed on your 
PC. 
I have also tried to integrate the Bio.Align.Generic alignment object sothat 
the Hmmer object is able to handle alignment objects by writing the records 
of the alignment object to a temporary fasta file. 

Since I have to write this up as a report I would greatly appreciate any 
criticism of any kind and perhaps some suggestions as to how I might improve 
the code. Also, If you can think of any other ways to implement the Hmmer 
stuff please let me know. 

At the moment I am working on a test suite for the project. If you would like 
the code I have written to exercise some of the methods please let me know 
and I'll send it over. 
I also have a bit of documentation I would like to add to the Application 
package because I feel if failed to help me concerning certain aspects. How 
would I go about this?

I look forward to hearing your suggestions. 

Glen van Ginkel
(Continue reading)

Glen van Ginkel | 12 Apr 11:10 2005
Picon

Hmmer API

This is a desperate-ish plea to any biopython developer.

Recently submitted an explanation of code that interacts with the Hmmer
(Eddy 2003) suite of programs to the list. I am required to write up a
project concerning this Hmmer API and would hugely appreciate it if ANY of
the developers could give me some feed-back. Bearing in mind that this is in
your spare time, I'm not asking for a major commentary. The focus of the
project was to produce something that might be accepted as part of the
BioPython project. What I'm looking for is just a sort of "yeah probably
will be accepted but.." or "No! you've got a long way to go before we accept
that gubbins, but.". 

I would really appreciate ANY response

In anticipation

Glen van Ginkel
Frank Kauff | 12 Apr 14:59 2005

Re: Hmmer API

Glen,

I'd be happy to have a look at it. I was recently thinking of using
Hmmer to do some alignment for one of my python scripts, so maybe your
API comes in handy. I'm not too familiar with Hmmer yet, though. So I
hope it comes with some example code...?

And thanks for contributing to biopython! 

Frank

On Tue, 2005-04-12 at 10:10 +0100, Glen van Ginkel wrote:
> This is a desperate-ish plea to any biopython developer.
> 
>  
> 
> Recently submitted an explanation of code that interacts with the Hmmer
> (Eddy 2003) suite of programs to the list. I am required to write up a
> project concerning this Hmmer API and would hugely appreciate it if ANY of
> the developers could give me some feed-back. Bearing in mind that this is in
> your spare time, I'm not asking for a major commentary. The focus of the
> project was to produce something that might be accepted as part of the
> BioPython project. What I'm looking for is just a sort of "yeah probably
> will be accepted but.." or "No! you've got a long way to go before we accept
> that gubbins, but.". 
> 
>  
> 
> I would really appreciate ANY response
> 
(Continue reading)

Jason A. Hackney | 12 Apr 22:20 2005
Picon

Re: Hmmer API

Hi Glen,

I would also be willing to have a look at any code you've got so far. 
I've done a bit of Hmmer stuff in the past, so I'd be interested in 
seeing what you've got going.

Cheers,

Jason

On Apr 12, 2005, at 2:10 AM, Glen van Ginkel wrote:

> This is a desperate-ish plea to any biopython developer.
>
>
>
> Recently submitted an explanation of code that interacts with the Hmmer
> (Eddy 2003) suite of programs to the list. I am required to write up a
> project concerning this Hmmer API and would hugely appreciate it if 
> ANY of
> the developers could give me some feed-back. Bearing in mind that this 
> is in
> your spare time, I'm not asking for a major commentary. The focus of 
> the
> project was to produce something that might be accepted as part of the
> BioPython project. What I'm looking for is just a sort of "yeah 
> probably
> will be accepted but.." or "No! you've got a long way to go before we 
> accept
> that gubbins, but.".
(Continue reading)

Iddo Friedberg | 13 Apr 00:34 2005

Re: Hmmer API

hi Folks,

Glen actually gave me the code, but I cannot really give him the 
response it merits, not within th time frame he would like. From a 
cursory look it is "yes, we can accept it, give us contingency tests as 
well". But if soeone can actually run it a couple of times, and see what 
it's like, that would be great.

Sorry Glen, I didn't realize you were that pressed for time.

Cheers,

Iddo

Glen van Ginkel wrote:

>This is a desperate-ish plea to any biopython developer.
>
> 
>
>Recently submitted an explanation of code that interacts with the Hmmer
>(Eddy 2003) suite of programs to the list. I am required to write up a
>project concerning this Hmmer API and would hugely appreciate it if ANY of
>the developers could give me some feed-back. Bearing in mind that this is in
>your spare time, I'm not asking for a major commentary. The focus of the
>project was to produce something that might be accepted as part of the
>BioPython project. What I'm looking for is just a sort of "yeah probably
>will be accepted but.." or "No! you've got a long way to go before we accept
>that gubbins, but.". 
>
(Continue reading)

Iddo Friedberg | 15 Apr 02:53 2005

[BioPython] Speakers for BOSC needed

Hi all,

It's that time of year again, and BOSC 2005 will be happening on June 
23-24. The more Biopython representatives, the merrier. I will be 
around, but I will be dealing with my own SIG meeting, so I will not be 
able to give a talk. Is there someone who can give the BioPython 
"plenary"? should be a 30-40 minute talk. Also, there are slots for 
shorter talks, so if you contributed and interesting module, or had an 
interesting experience with biopython you would like to share, please 
submit a talk.

For those of you who do not know what BOSC is, it's the Bioinformatics 
Open Source Conference, which is held as a satellite meeting of ISMB. I 
highly recommend this event, it is a real eye opener with respect to the 
world of open source, and computational biology. More about it here:

http://open-bio.org/bosc/

Cheers,

Iddo

--

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
http://ffas.ljcrf.edu/~iddo
==========================
(Continue reading)

Darin London | 19 Apr 11:16 2005
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Re: BOSC 2005

{Please pass the word!}

SECOND CALL FOR SPEAKERS

The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the
not-for-profit Open Bioinformatics Foundation. The meeting will take place
June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest
Group (SIG) meetings occurring in conjunction with the 13th International Conference
on Intelligent Systems for Molecular Biology.

see http://www.iscb.org/ismb2005 for more information.

Because of the power of many Open Source bioinformatics packages in
use by the Research Community today, it is not too presumptuous to say 
that the work of the Open Source Bioinformatics Community represents 
the cutting edge of Bioinformatics in general. This has been repeatedly 
demonstrated by the quality of presentations at previous BOSC conferences.
This year, at BOSC 2005, we want to continue this tradition of excellence, 
while presenting this message to a wider part of the Research Community.  
Please, pass this message on to anyone you know that is interested in
Bioinformatics software. 

 
BOSC PROGRAM & CONTACT INFO

* Web: http://www.open-bio.org/bosc2005/
* Online Registration: https://www.cteusa.com/iscb4/
* Email: bosc@...

FEES
(Continue reading)


Gmane