From biopython at maubp.freeserve.co.uk  Thu Nov 26 11:02:50 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Nov 2009 16:02:50 +0000
Subject: [emboss-dev] Fwd: [DAS] DAS workshop 7th-9th April 2010
In-Reply-To: <F30A9ED7-41E9-4833-A094-FDF0893E0F92@sanger.ac.uk>
References: <F30A9ED7-41E9-4833-A094-FDF0893E0F92@sanger.ac.uk>
Message-ID: <320fb6e00911260802wb98b28fic8a193c125e29d9c@mail.gmail.com>

This might be of interest to some of you.

Peter

---------- Forwarded message ----------
From: Jonathan Warren <jw12 at sanger.ac.uk>
Date: Thu, Nov 26, 2009 at 2:57 PM
Subject: [DAS] DAS workshop 7th-9th April 2010
To: das at biodas.org, das_registry_announce at sanger.ac.uk, biojava-dev
<biojava-dev at biojava.org>, BioJava <biojava-l at biojava.org>, BioPerl
<bioperl-l at lists.open-bio.org>, all at sanger.ac.uk, all at ebi.ac.uk,
ensembldev <ensembl-dev at ebi.ac.uk>



We are considering running a Distributed Annotation System workshop
here at the Sanger/EBI in the UK subject to decent demand.
The workshop will be held from Wednesday 7th-Friday 9th April 2010. If
you would be interested in attending either to present or just take
part
then please email me jw12 at sanger.ac.uk

The format of the workshop is likely to be similar to last years (1st
day for beginners, 2nd for both beginners and advanced users, 3rd day
for advanced), information for which can be found here:
http://www.dasregistry.org/course.jsp

If you would like to present then please send a short summary of what
you would like to talk about.

Thanks

Jonathan.

Jonathan Warren
Senior Developer and DAS coordinator
jw12 at sanger.ac.uk









--
The Wellcome Trust Sanger Institute is operated by Genome
ResearchLimited, a charity registered in England with number 1021457
and acompany registered in England with number 2742969, whose
registeredoffice is 215 Euston Road, London, NW1
2BE._______________________________________________
DAS mailing list
DAS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/das

From pjotr.public78 at thebird.nl  Mon Nov 30 05:03:27 2009
From: pjotr.public78 at thebird.nl (Pjotr Prins)
Date: Mon, 30 Nov 2009 11:03:27 +0100
Subject: [emboss-dev] Mapping EMBOSS to Ruby, Perl and Python
Message-ID: <20091130100327.GA6857@thebird.nl>

Hi all,

I have started mapping some to the EMBOSS functions using Biolib. For
a write up see: 

  http://biolib.open-bio.org/wiki/Mapping_EMBOSS

Also I have migrated the CVS repository to git - it is hosted at

  http://github.com/pjotrp/EMBOSS 
  
and includes the whole CVS version history. I would strongly recommend
using git(hub) over CVS. In my experience it is much nicer to work
with and collaborate.

The next EMBOSS function I wish to map is 'getorf'. However, much of
the logic is in the main() routine. I'll try and move the logic out,
so an emboss_getorf() function is exported to Ruby (Perl and Python).

I'll send a patch for examination.

Pjotr Prins
Wageningen University

P.S. Note that Biolib maps the current EMBOSS tree ... !(*stable_6.1.0)

From pjotr.public78 at thebird.nl  Mon Nov 30 06:57:17 2009
From: pjotr.public78 at thebird.nl (Pjotr Prins)
Date: Mon, 30 Nov 2009 12:57:17 +0100
Subject: [emboss-dev] Mapping EMBOSS to Ruby, Perl and Python
Message-ID: <20091130115717.GA9235@thebird.nl>

For your inspection, I have committed a patch for splitting out the
logic of ./emboss/transeq.c. The patch is here:

  http://github.com/pjotrp/EMBOSS/commit/713800c4aa08ddf70b87f245a524c1a0b30c0942

The simplified transeq.c is here:

  http://github.com/pjotrp/EMBOSS/blob/biolib/emboss/transeq.c

The new interfaces are here:

  http://github.com/pjotrp/EMBOSS/blob/biolib/emboss/function/emboss_transeq.c

Basically I have split out the ACD logic and programming logic and
given them new names:

  int transeq_acd(int argc, char **argv)

  AjPSeqout transeq( AjPSeqall seqall, AjPStr *framelist, AjPStr tablename, AjPRange regions, AjBool trim, AjBool clean, AjBool alternate)

so you can call either from an external program. The advantage being
the call interface is exactly the same, whether from the command
line, the web interface, or directly through a shared linked library.

What do you think? I propose to (slowly) accept splitting out the
other routines in this fashion. As it does not interfere with EMBOSS
it can be done in small steps.

The file emboss/function/emboss_transeq.c may get some extra
interfaces - the idea is that is contains nicely named and direct
methods (unlike the internal 'ajCamelCase' naming conventions). A
useful one would be a simple one reading frame translation with
pre-selected translation table (for speed). But more on that later -
I can also weight-lift that in biolib itself.

The reason I want to do this here is to prevent duplication of
functionality at different levels. 

Pj.

From biopython at maubp.freeserve.co.uk  Thu Nov 26 16:02:50 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 26 Nov 2009 16:02:50 +0000
Subject: [emboss-dev] Fwd: [DAS] DAS workshop 7th-9th April 2010
In-Reply-To: <F30A9ED7-41E9-4833-A094-FDF0893E0F92@sanger.ac.uk>
References: <F30A9ED7-41E9-4833-A094-FDF0893E0F92@sanger.ac.uk>
Message-ID: <320fb6e00911260802wb98b28fic8a193c125e29d9c@mail.gmail.com>

This might be of interest to some of you.

Peter

---------- Forwarded message ----------
From: Jonathan Warren <jw12 at sanger.ac.uk>
Date: Thu, Nov 26, 2009 at 2:57 PM
Subject: [DAS] DAS workshop 7th-9th April 2010
To: das at biodas.org, das_registry_announce at sanger.ac.uk, biojava-dev
<biojava-dev at biojava.org>, BioJava <biojava-l at biojava.org>, BioPerl
<bioperl-l at lists.open-bio.org>, all at sanger.ac.uk, all at ebi.ac.uk,
ensembldev <ensembl-dev at ebi.ac.uk>



We are considering running a Distributed Annotation System workshop
here at the Sanger/EBI in the UK subject to decent demand.
The workshop will be held from Wednesday 7th-Friday 9th April 2010. If
you would be interested in attending either to present or just take
part
then please email me jw12 at sanger.ac.uk

The format of the workshop is likely to be similar to last years (1st
day for beginners, 2nd for both beginners and advanced users, 3rd day
for advanced), information for which can be found here:
http://www.dasregistry.org/course.jsp

If you would like to present then please send a short summary of what
you would like to talk about.

Thanks

Jonathan.

Jonathan Warren
Senior Developer and DAS coordinator
jw12 at sanger.ac.uk









--
The Wellcome Trust Sanger Institute is operated by Genome
ResearchLimited, a charity registered in England with number 1021457
and acompany registered in England with number 2742969, whose
registeredoffice is 215 Euston Road, London, NW1
2BE._______________________________________________
DAS mailing list
DAS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/das


From pjotr.public78 at thebird.nl  Mon Nov 30 10:03:27 2009
From: pjotr.public78 at thebird.nl (Pjotr Prins)
Date: Mon, 30 Nov 2009 11:03:27 +0100
Subject: [emboss-dev] Mapping EMBOSS to Ruby, Perl and Python
Message-ID: <20091130100327.GA6857@thebird.nl>

Hi all,

I have started mapping some to the EMBOSS functions using Biolib. For
a write up see: 

  http://biolib.open-bio.org/wiki/Mapping_EMBOSS

Also I have migrated the CVS repository to git - it is hosted at

  http://github.com/pjotrp/EMBOSS 
  
and includes the whole CVS version history. I would strongly recommend
using git(hub) over CVS. In my experience it is much nicer to work
with and collaborate.

The next EMBOSS function I wish to map is 'getorf'. However, much of
the logic is in the main() routine. I'll try and move the logic out,
so an emboss_getorf() function is exported to Ruby (Perl and Python).

I'll send a patch for examination.

Pjotr Prins
Wageningen University

P.S. Note that Biolib maps the current EMBOSS tree ... !(*stable_6.1.0)


From pjotr.public78 at thebird.nl  Mon Nov 30 11:57:17 2009
From: pjotr.public78 at thebird.nl (Pjotr Prins)
Date: Mon, 30 Nov 2009 12:57:17 +0100
Subject: [emboss-dev] Mapping EMBOSS to Ruby, Perl and Python
Message-ID: <20091130115717.GA9235@thebird.nl>

For your inspection, I have committed a patch for splitting out the
logic of ./emboss/transeq.c. The patch is here:

  http://github.com/pjotrp/EMBOSS/commit/713800c4aa08ddf70b87f245a524c1a0b30c0942

The simplified transeq.c is here:

  http://github.com/pjotrp/EMBOSS/blob/biolib/emboss/transeq.c

The new interfaces are here:

  http://github.com/pjotrp/EMBOSS/blob/biolib/emboss/function/emboss_transeq.c

Basically I have split out the ACD logic and programming logic and
given them new names:

  int transeq_acd(int argc, char **argv)

  AjPSeqout transeq( AjPSeqall seqall, AjPStr *framelist, AjPStr tablename, AjPRange regions, AjBool trim, AjBool clean, AjBool alternate)

so you can call either from an external program. The advantage being
the call interface is exactly the same, whether from the command
line, the web interface, or directly through a shared linked library.

What do you think? I propose to (slowly) accept splitting out the
other routines in this fashion. As it does not interfere with EMBOSS
it can be done in small steps.

The file emboss/function/emboss_transeq.c may get some extra
interfaces - the idea is that is contains nicely named and direct
methods (unlike the internal 'ajCamelCase' naming conventions). A
useful one would be a simple one reading frame translation with
pre-selected translation table (for speed). But more on that later -
I can also weight-lift that in biolib itself.

The reason I want to do this here is to prevent duplication of
functionality at different levels. 

Pj.