From email2ants at gmail.com  Thu Oct  2 13:16:04 2008
From: email2ants at gmail.com (Anthony Underwood)
Date: Thu, 2 Oct 2008 18:16:04 +0100
Subject: [BioRuby] trace files (scf/abi) and ruby/bioruby
Message-ID: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>

Hi all,

Does anybody know if there is or someone is working on a ruby module  
for reading abi/scf trace files. I was thinking of perhaps having a go  
at this but thought I would check that there is no work in progress  
that I should know about. I have done a few Google searches but come  
up with nothing so thought I would ask on this list as well.

Many thanks

Anthony

From jan.aerts at gmail.com  Thu Oct  2 14:04:45 2008
From: jan.aerts at gmail.com (Jan Aerts)
Date: Thu, 2 Oct 2008 19:04:45 +0100
Subject: [BioRuby] trace files (scf/abi) and ruby/bioruby
In-Reply-To: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>
References: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>
Message-ID: <4c7507a70810021104v7fd9c09dx57e317c2573e60a7@mail.gmail.com>

If there's nothing there yet, you might have a look at the bioperl version
and take that as a guide.

jan.

2008/10/2 Anthony Underwood <email2ants at gmail.com>

> Hi all,
>
> Does anybody know if there is or someone is working on a ruby module for
> reading abi/scf trace files. I was thinking of perhaps having a go at this
> but thought I would check that there is no work in progress that I should
> know about. I have done a few Google searches but come up with nothing so
> thought I would ask on this list as well.
>
> Many thanks
>
> Anthony
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

From ngoto at gen-info.osaka-u.ac.jp  Thu Oct  2 23:42:09 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Fri, 3 Oct 2008 12:42:09 +0900
Subject: [BioRuby] trace files (scf/abi) and ruby/bioruby
In-Reply-To: <4c7507a70810021104v7fd9c09dx57e317c2573e60a7@mail.gmail.com>
References: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>
	<4c7507a70810021104v7fd9c09dx57e317c2573e60a7@mail.gmail.com>
Message-ID: <20081003034209.939C81CBC434@idnmail.gen-info.osaka-u.ac.jp>

Hi,

For ABI traces, as far as I know, some person made previously, 
but all codes are lost now.

http://open-bio.org/pipermail/bioruby/2005-September/000128.html
but I cannot access to the URL described in the above archive.

I don't remember why it wasn't included in bioruby, but,
the thread of ML archive suggests that no one made any efforts
to change the code adopting the development guideline.

As Jan says, looking at bioperl, biopython, biojava, Staden, etc.
and to write your own code seems good.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 2 Oct 2008 19:04:45 +0100
"Jan Aerts" <jan.aerts at gmail.com> wrote:

> If there's nothing there yet, you might have a look at the bioperl version
> and take that as a guide.
> 
> jan.
> 
> 2008/10/2 Anthony Underwood <email2ants at gmail.com>
> 
> > Hi all,
> >
> > Does anybody know if there is or someone is working on a ruby module for
> > reading abi/scf trace files. I was thinking of perhaps having a go at this
> > but thought I would check that there is no work in progress that I should
> > know about. I have done a few Google searches but come up with nothing so
> > thought I would ask on this list as well.
> >
> > Many thanks
> >
> > Anthony
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From jan.aerts at gmail.com  Fri Oct  3 13:05:28 2008
From: jan.aerts at gmail.com (Jan Aerts)
Date: Fri, 3 Oct 2008 18:05:28 +0100
Subject: [BioRuby] ruby API to ensembl database
Message-ID: <4c7507a70810031005t2fa4864ct850c7769eb2b372a@mail.gmail.com>

All,

Just to let you know that we updated the Ensembl ruby API so that it also
works for version 50. There are no different APIs for each release of the
database; just mention the release number in your connection. In addition to
core, Francesco Strozzi has been working on the API for the variation
database, the first version of which is now also available.

In addition to the API itself, the latest release also contains an 'ensembl'
executable that will drop you in interactive ruby (irb) already connected to
one of the databases. Just run "ensembl homo_sapiens 50".

Development is on the github site at
http://github.com/jandot/ruby-ensembl-api. The API documentation and
tutorial are at http://www.sanger.ac.uk/Users/ja8/. To install: download the
gem from the github site and run "gem install ruby-ensembl-api-0.9.2.gem".

Small sample of script using the API:
<begin of sample>

DBConnection.connect('homo_sapiens')

slice = Slice.fetch_by_region('chromosome','4',10000,99999,-1)
slice.genes.each do |gene|
  puts gene.stable_id + "\t" + gene.status + "\t" + gene.slice.display_name
end


<end of sample>

jan.

From sebe at nmr.mpibpc.mpg.de  Tue Oct  7 03:22:00 2008
From: sebe at nmr.mpibpc.mpg.de (Sebastian Becker)
Date: Tue, 7 Oct 2008 09:22:00 +0200
Subject: [BioRuby] isoelctric point for proteins
Message-ID: <34683B72-8C2D-4C39-8856-A084F903918A@nmr.mpibpc.mpg.de>

Hi folks,

I am wondering if there is a module in BioRuby for calculating the  
iep (isoelectric point) for proteins?
I appreciate all infos.

Cheers
Sebastian

From matias.piipari at gmail.com  Tue Oct  7 10:17:02 2008
From: matias.piipari at gmail.com (Matias Piipari)
Date: Tue, 7 Oct 2008 15:17:02 +0100
Subject: [BioRuby] Querying the NCBI taxonomy with bioruby?
Message-ID: <15cdf3360810070717uee04bc8ra2ef66fe6e7f6ced@mail.gmail.com>

Is it possible to query organism names that match a given NCBI taxonomy ID
with bioruby? My API doc searches haven't uncovered anything like this for
querying the taxonomy at least, but just thought I'd check before I write it
myself.

Thanks,
Matias

From donttrustben at gmail.com  Fri Oct 10 00:18:32 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Fri, 10 Oct 2008 15:18:32 +1100
Subject: [BioRuby] URL Generation in Bioruby
Message-ID: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>

Hi list,

A common thing I find myself doing is to 'linkout' to other databases. For
instance, I have a PDB id and I want to link to the corresponding record in
pdb.org. Right now, I would have to go to the pdb site and try to reverse
engineer it. In the past I've even had to email the webmasters for more
information. It seems to me this is a duplication of effort, and so
class(es) to collect this information for me might have a place in BioRuby.

Does this sound reasonable to anyone? Is there any precendents out there?
What might be a good way to structure the code?

Thanks,
ben

-- 
FYI: My email addresses at unimelb, uq and gmail all redirect to the same
place.

From donttrustben at gmail.com  Fri Oct 10 18:28:47 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Sat, 11 Oct 2008 09:28:47 +1100
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
Message-ID: <bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>

Thanks for your response. I would have thought the fact that they change is
more reason to include it - not less.

Is that database you speak of freely available? Just as part of the AceDB
download?

Thanks,
ben

2008/10/10 Michael Han <mh6 at sanger.ac.uk>

>
> On 10 Oct 2008, at 05:18, Ben Woodcroft wrote:
>
> Hi list,
>
> A common thing I find myself doing is to 'linkout' to other databases. For
> instance, I have a PDB id and I want to link to the corresponding record in
> pdb.org. Right now, I would have to go to the pdb site and try to reverse
> engineer it. In the past I've even had to email the webmasters for more
> information. It seems to me this is a duplication of effort, and so
> class(es) to collect this information for me might have a place in BioRuby.
>
> Does this sound reasonable to anyone? Is there any precendents out there?
> What might be a good way to structure the code?
>
> Thanks,
> ben
>
> --
> FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> place.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>
>
> Hi Ben,
>
> what we did is save URL constructors in an database object in a sprintf
> style, which is in turn used by the xref objects linked to
> genes/proteins/etc.
> Anyway I am not sure if it is a good idea to put it in the bioruby library,
> as when you have a couple of dozens of different database, you can be sure
> that one URL will change every few days/weeks, so it is a hassle to keep all
> of them up-to-date.
> Michael
> ---------------------------------------
>   oo Wormbase Group, Sanger Institute
>   |  The Wellcome Trust Genome Campus,
>   |  Hinxton, Cambridge, CB10 1HH, UK.
>   |  Tel.: +44 (0)1223 49 6869
> --'
>
>
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose registered office is 215
> Euston Road, London, NW1 2BE.
>



-- 
FYI: My email addresses at unimelb, uq and gmail all redirect to the same
place.

From pjotr2008 at thebird.nl  Sat Oct 11 03:54:40 2008
From: pjotr2008 at thebird.nl (Pjotr Prins)
Date: Sat, 11 Oct 2008 09:54:40 +0200
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
	<bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
Message-ID: <20081011075440.GA19106@thebird.nl>

We could have a mixin module with methods that generate all different
URLs in a central location. I think that is a good idea.

Pj.

On Sat, Oct 11, 2008 at 09:28:47AM +1100, Ben Woodcroft wrote:
> Thanks for your response. I would have thought the fact that they change is
> more reason to include it - not less.
> 
> Is that database you speak of freely available? Just as part of the AceDB
> download?
> 
> Thanks,
> ben
> 
> 2008/10/10 Michael Han <mh6 at sanger.ac.uk>
> 
> >
> > On 10 Oct 2008, at 05:18, Ben Woodcroft wrote:
> >
> > Hi list,
> >
> > A common thing I find myself doing is to 'linkout' to other databases. For
> > instance, I have a PDB id and I want to link to the corresponding record in
> > pdb.org. Right now, I would have to go to the pdb site and try to reverse
> > engineer it. In the past I've even had to email the webmasters for more
> > information. It seems to me this is a duplication of effort, and so
> > class(es) to collect this information for me might have a place in BioRuby.
> >
> > Does this sound reasonable to anyone? Is there any precendents out there?
> > What might be a good way to structure the code?
> >
> > Thanks,
> > ben
> >
> > --
> > FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> > place.
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> >
> > Hi Ben,
> >
> > what we did is save URL constructors in an database object in a sprintf
> > style, which is in turn used by the xref objects linked to
> > genes/proteins/etc.
> > Anyway I am not sure if it is a good idea to put it in the bioruby library,
> > as when you have a couple of dozens of different database, you can be sure
> > that one URL will change every few days/weeks, so it is a hassle to keep all
> > of them up-to-date.
> > Michael
> > ---------------------------------------
> >   oo Wormbase Group, Sanger Institute
> >   |  The Wellcome Trust Genome Campus,
> >   |  Hinxton, Cambridge, CB10 1HH, UK.
> >   |  Tel.: +44 (0)1223 49 6869
> > --'
> >
> >
> >
> >
> > -- The Wellcome Trust Sanger Institute is operated by Genome Research
> > Limited, a charity registered in England with number 1021457 and a company
> > registered in England with number 2742969, whose registered office is 215
> > Euston Road, London, NW1 2BE.
> >
> 
> 
> 
> -- 
> FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> place.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

From davide.rambaldi at ifom-ieo-campus.it  Sun Oct 12 11:10:14 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Sun, 12 Oct 2008 17:10:14 +0200
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <20080926133733.A99061CBC3F0@idnmail.gen-info.osaka-u.ac.jp>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<992DF6FE-14DF-45B9-B141-224FF473E82B@hgc.jp>
	<6B068F99-56FA-4E7E-AB60-887B83480F05@ifom-ieo-campus.it>
	<20080926133733.A99061CBC3F0@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <9A8CA4BF-5DEE-402A-9A89-E266F139F0F9@ifom-ieo-campus.it>


Il giorno 26/set/08, alle ore 15:37, Naohisa GOTO ha scritto:

> Thank you for a patch, but it has some problems:
> For KEGG API, $?.exitstatus has no mean, and no need to check $?.
> The "AF237819" should not be hardcoded because the method is
> not only for demo, but a bioruby-shell command to fetch entry
> specified by a user. Also note that "db" => "nuccore" would
> not always be good. (If result is empty, switching to another
> database and trying again would be the best way.)


I apologize for this.... was really stupid and sorry for the late  
answer (my laptop have died... with all my bioruby test inside)

Maybe I can propose anther patch: the patch to bio.rb add an autoload  
call for Bio::NCBI::REST in bio.rb, the patch to bio/shell/plugin/ 
entry.rb don't have the entry hardcoded.

About the entry.rb patch I have two questions:

- I put the db prefix (demo is gb:AF237819) to define the rettype for  
NCBI::REST. Work for the demo. but I guess this should be changed...

- For the database I have used the general db "sequences", assuming  
that the method getent of entry.rb is only for sequences... is this  
correct?


PATCHES:

diff --git a/lib/bio.rb b/lib/bio.rb
index b2b6f4f..bddc221 100644
--- a/lib/bio.rb
+++ b/lib/bio.rb
@@ -170,6 +170,7 @@ module Bio

    class NCBI
      autoload :SOAP,       'bio/io/ncbisoap'
+    autoload :REST,       'bio/io/ncbirest'
    end


diff --git a/lib/bio/shell/plugin/entry.rb b/lib/bio/shell/plugin/ 
entry.rb
index 6d36fb5..21ef9f6 100644
--- a/lib/bio/shell/plugin/entry.rb
+++ b/lib/bio/shell/plugin/entry.rb
@@ -88,8 +88,14 @@ module Bio::Shell

        # KEGG API at http://www.genome.jp/kegg/soap/
        else
-        puts "Retrieving entry from KEGG API (#{arg})"
          entry = bget(arg)
+        if entry.length != 0 then
+          puts "Retrieving entry from KEGG API (#{arg})"
+        else
+          puts "Retrieving entry from NCBI (#{arg})"
+          fetch = Bio::NCBI::REST.efetch(entry_id,  
{"db"=>"sequences", "rettype"=>db})
+          entry = fetch.to_s
+        end
        end
      end


Best Regards.



Davide Rambaldi,
Bioinformatics PhD student.
-----------------------------------------------------
Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy

[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi  
(homepage)
[i] http://www.semm.it             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)

-----------------------------------------------------





From davide.rambaldi at ifom-ieo-campus.it  Mon Oct 13 08:34:18 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Mon, 13 Oct 2008 14:34:18 +0200
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
Message-ID: <3D8E9D1A-CB03-46C5-B2F5-6FD46D96A4CD@ifom-ieo-campus.it>

Hi all,

the machine is an Intel Darwin 9.5.0 (MAC OSX 10.5.5), is the super  
desktop m boss give me at the lab.... (wow)

MAC OS X 10.5 came with ruby embedded in Developer tools.

Here is the gem env:

RubyGems Environment:
   - RUBYGEMS VERSION: 1.0.1 (1.0.1)
   - RUBY VERSION: 1.8.6 (2008-03-03 patchlevel 114) [universal- 
darwin9.0]
   - INSTALLATION DIRECTORY: /Library/Ruby/Gems/1.8
   - RUBYGEMS PREFIX: /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/lib/ruby
   - RUBY EXECUTABLE: /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/ruby
   - RUBYGEMS PLATFORMS:
     - ruby
     - universal-darwin-9
   - GEM PATHS:
      - /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ 
ruby/gems/1.8
      - /Library/Ruby/Gems/1.8
   - GEM CONFIGURATION:
      - :update_sources => true
      - :verbose => true
      - :benchmark => false
      - :backtrace => false
      - :bulk_threshold => 1000
   - REMOTE SOURCES:
      - http://gems.rubyforge.org



You may notice that installation directory are under /System/Library/ 
Frameworks/...    (you know: mac like to make developer life more  
complicated)

So now I retrieve the last bioruby from git with: git clone git:// 
github.com/bioruby/bioruby.git

I enter dir and I install in the canonical way:

ruby install.rb config
ruby install.rb setup


At this point the config.save file (is the file that stoe the urrent  
configuration sure?) contains:

bin-dir=$prefix/bin
prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
ruby-path=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
bin/ruby
make-prog=make
rb-dir=$site-ruby
without-ext=no
ruby-prog=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
bin/ruby
std-ruby=$prefix/lib/ruby/1.8
data-dir=$prefix/share


So all seems ok but when I try to install with:

sudo ruby install.rb install


install.rb: entering install phase...
---> bin
mkdir -p /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
install bioruby /System/Library/Frameworks/Ruby.framework/Versions/1.8/ 
usr/bin/
install br_biofetch.rb /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/
install br_bioflat.rb /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/
install br_biogetseq.rb /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/
install br_pmfetch.rb /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/
<--- bin
---> lib
mkdir -p /
install bio.rb /
---> lib/bio
mkdir -p /bio

[...] (continue)


ARGH!!!! after the bin install the install.rb install ALL the bio  
library in ROOT!

So to summarize:

- first bin are install correctly in /System/Library/.../usr/bin
- the ENTIRE library is installed in the wrong PATH (/)

Please notice that in another MAC with 10.5 really similar BUT with a  
manual installed version of ruby 1.8.7 in /url/local/bin the  
installation of bioruby is correct and all is installed in the correct  
path (in that case /usr/local/lib)

To conclude seems that there is a BUG in install.rb that is unable to  
install the bioruby library in /System/Library/Frameworks/ 
Ruby.framework/Version/1.8/usr/lib

If you don't have a MAC for testing, I can try to fix this, just give  
me some clues.

I have tried to specify the prefix with:

ruby install.rb setup --prefix=/System/Library/Frameworks/ 
Ruby.framework/Versions/1.8/usr

but in installation I have the same problem that is summarized by this  
2 lines of the install log!:

mkdir -p /
install bio.rb /


Again I can help you fix this, cause I have the right MAC to make  
tests, but I have no clues of where is the bug....


Best Regards


Davide Rambaldi, Bioinformatics PhD student.
-----------------------------------------------------
Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy
[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it 
 >
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi < 
%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi>  
(homepage)
[i] http://www.semm.it <http://www.semm.it/>             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)
-----------------------------------------------------


From adamnkraut at gmail.com  Mon Oct 13 10:07:07 2008
From: adamnkraut at gmail.com (Adam Kraut)
Date: Mon, 13 Oct 2008 10:07:07 -0400
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
In-Reply-To: <3D8E9D1A-CB03-46C5-B2F5-6FD46D96A4CD@ifom-ieo-campus.it>
References: <3D8E9D1A-CB03-46C5-B2F5-6FD46D96A4CD@ifom-ieo-campus.it>
Message-ID: <134ede0b0810130707j1315b8b2p40a4c423a353416e@mail.gmail.com>

Hi Davide,

Have you tried using the --prefix option for the 'install' command?  The
prefix only applies to the install task according to the help.  This appears
to be working OK for me on 10.5.5

/usr/bin/ruby install.rb install
--prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr

Note that I personally compile my own Ruby in /usr/local and don't recommend
using the Ruby supplied by Apple.  YMMV.

-Adam

On Mon, Oct 13, 2008 at 8:34 AM, Davide Rambaldi <
davide.rambaldi at ifom-ieo-campus.it> wrote:

> Hi all,
>
> the machine is an Intel Darwin 9.5.0 (MAC OSX 10.5.5), is the super desktop
> m boss give me at the lab.... (wow)
>
> MAC OS X 10.5 came with ruby embedded in Developer tools.
>
> Here is the gem env:
>
> RubyGems Environment:
>  - RUBYGEMS VERSION: 1.0.1 (1.0.1)
>  - RUBY VERSION: 1.8.6 (2008-03-03 patchlevel 114) [universal-darwin9.0]
>  - INSTALLATION DIRECTORY: /Library/Ruby/Gems/1.8
>  - RUBYGEMS PREFIX:
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby
>  - RUBY EXECUTABLE:
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
>  - RUBYGEMS PLATFORMS:
>    - ruby
>    - universal-darwin-9
>  - GEM PATHS:
>     -
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8
>     - /Library/Ruby/Gems/1.8
>  - GEM CONFIGURATION:
>     - :update_sources => true
>     - :verbose => true
>     - :benchmark => false
>     - :backtrace => false
>     - :bulk_threshold => 1000
>  - REMOTE SOURCES:
>     - http://gems.rubyforge.org
>
>
>
> You may notice that installation directory are under
> /System/Library/Frameworks/...    (you know: mac like to make developer life
> more complicated)
>
> So now I retrieve the last bioruby from git with: git clone git://
> github.com/bioruby/bioruby.git
>
> I enter dir and I install in the canonical way:
>
> ruby install.rb config
> ruby install.rb setup
>
>
> At this point the config.save file (is the file that stoe the urrent
> configuration sure?) contains:
>
> bin-dir=$prefix/bin
> prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
>
> ruby-path=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> make-prog=make
> rb-dir=$site-ruby
> without-ext=no
>
> ruby-prog=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> std-ruby=$prefix/lib/ruby/1.8
> data-dir=$prefix/share
>
>
> So all seems ok but when I try to install with:
>
> sudo ruby install.rb install
>
>
> install.rb: entering install phase...
> ---> bin
> mkdir -p /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install bioruby
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_biofetch.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_bioflat.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_biogetseq.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_pmfetch.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> <--- bin
> ---> lib
> mkdir -p /
> install bio.rb /
> ---> lib/bio
> mkdir -p /bio
>
> [...] (continue)
>
>
> ARGH!!!! after the bin install the install.rb install ALL the bio library
> in ROOT!
>
> So to summarize:
>
> - first bin are install correctly in /System/Library/.../usr/bin
> - the ENTIRE library is installed in the wrong PATH (/)
>
> Please notice that in another MAC with 10.5 really similar BUT with a
> manual installed version of ruby 1.8.7 in /url/local/bin the installation of
> bioruby is correct and all is installed in the correct path (in that case
> /usr/local/lib)
>
> To conclude seems that there is a BUG in install.rb that is unable to
> install the bioruby library in
> /System/Library/Frameworks/Ruby.framework/Version/1.8/usr/lib
>
> If you don't have a MAC for testing, I can try to fix this, just give me
> some clues.
>
> I have tried to specify the prefix with:
>
> ruby install.rb setup
> --prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
>
> but in installation I have the same problem that is summarized by this 2
> lines of the install log!:
>
> mkdir -p /
> install bio.rb /
>
>
> Again I can help you fix this, cause I have the right MAC to make tests,
> but I have no clues of where is the bug....
>
>
> Best Regards
>
>
> Davide Rambaldi, Bioinformatics PhD student.
> -----------------------------------------------------
> Bioinformatic Group IFOM-IEO Campus
> Via Adamello 16, Milano
> I-20139 Italy
> [t] +39 02574303 066
> [e] davide.rambaldi at ifom-ieo-campus.it <mailto:
> davide.rambaldi at ifom-ieo-campus.it>
> [i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi <%20
> http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi>
> (homepage)
> [i] http://www.semm.it <http://www.semm.it/>             (PhD school)
> [i] http://www.btbs.unimib.it/     (Master)
> -----------------------------------------------------
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby<https://lists.open-bio.org/mailman/listinfo/bioruby>
>

From davide.rambaldi at ifom-ieo-campus.it  Mon Oct 13 10:34:49 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Mon, 13 Oct 2008 16:34:49 +0200
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
In-Reply-To: <134ede0b0810130707j1315b8b2p40a4c423a353416e@mail.gmail.com>
References: <3D8E9D1A-CB03-46C5-B2F5-6FD46D96A4CD@ifom-ieo-campus.it>
	<134ede0b0810130707j1315b8b2p40a4c423a353416e@mail.gmail.com>
Message-ID: <8E8BC237-6E23-45F3-B516-14214653271D@ifom-ieo-campus.it>


On 13 Oct 2008, at 16:07, Adam Kraut wrote:

> Hi Davide,
>
> Have you tried using the --prefix option for the 'install' command?   
> The prefix only applies to the install task according to the help.   
> This appears to be working OK for me on 10.5.5
>
> /usr/bin/ruby install.rb install --prefix=/System/Library/Frameworks/ 
> Ruby.framework/Versions/1.8/usr


Yeah something similar (note the final lib) do the job:


sudo ruby install.rb install --prefix=/System/Library/Frameworks/ 
Ruby.framework/Versions/1.8/usr/lib/


BUT note the I have to specify also lib (or it will install in /System/ 
Library/Frameworks/Ruby.framework/Versions/1.8/usr/ an the library in  
unreachable)


NOW:


wst433:bioruby default$ irb
 >> require 'bio'
=> true


But (cause I have added the prefix /System/Library/Frameworks/ 
Ruby.framework/Versions/1.8/usr/lib/)

I have now the bin into:

/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/System/ 
Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/


terrible! :(

sigh

I hate MAC frameworks.....

>
>
> Note that I personally compile my own Ruby in /usr/local and don't  
> recommend using the Ruby supplied by Apple.  YMMV.
>

I am agree with you, and I have personally compiled my 1.8.7 ruby in / 
usr/local/bin

but may be is important to report the bug: automatic installation of  
bio.rb and bio directory in / (root) is painful for the general user

(imagine someone that see the error, want to remove /bio and for  
mistake type: sudo rm -rf / .... and the HD is gone! )



> -Adam
>
> On Mon, Oct 13, 2008 at 8:34 AM, Davide Rambaldi <davide.rambaldi at ifom-ieo-campus.it 
> > wrote:
> Hi all,
>
> the machine is an Intel Darwin 9.5.0 (MAC OSX 10.5.5), is the super  
> desktop m boss give me at the lab.... (wow)
>
> MAC OS X 10.5 came with ruby embedded in Developer tools.
>
> Here is the gem env:
>
> RubyGems Environment:
>  - RUBYGEMS VERSION: 1.0.1 (1.0.1)
>  - RUBY VERSION: 1.8.6 (2008-03-03 patchlevel 114) [universal- 
> darwin9.0]
>  - INSTALLATION DIRECTORY: /Library/Ruby/Gems/1.8
>  - RUBYGEMS PREFIX: /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/lib/ruby
>  - RUBY EXECUTABLE: /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/bin/ruby
>  - RUBYGEMS PLATFORMS:
>    - ruby
>    - universal-darwin-9
>  - GEM PATHS:
>     - /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ 
> ruby/gems/1.8
>     - /Library/Ruby/Gems/1.8
>  - GEM CONFIGURATION:
>     - :update_sources => true
>     - :verbose => true
>     - :benchmark => false
>     - :backtrace => false
>     - :bulk_threshold => 1000
>  - REMOTE SOURCES:
>     - http://gems.rubyforge.org
>
>
>
> You may notice that installation directory are under /System/Library/ 
> Frameworks/...    (you know: mac like to make developer life more  
> complicated)
>
> So now I retrieve the last bioruby from git with: git clone git:// 
> github.com/bioruby/bioruby.git
>
> I enter dir and I install in the canonical way:
>
> ruby install.rb config
> ruby install.rb setup
>
>
> At this point the config.save file (is the file that stoe the urrent  
> configuration sure?) contains:
>
> bin-dir=$prefix/bin
> prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> ruby-path=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
> bin/ruby
> make-prog=make
> rb-dir=$site-ruby
> without-ext=no
> ruby-prog=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
> bin/ruby
> std-ruby=$prefix/lib/ruby/1.8
> data-dir=$prefix/share
>
>
> So all seems ok but when I try to install with:
>
> sudo ruby install.rb install
>
>
> install.rb: entering install phase...
> ---> bin
> mkdir -p /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
> bin/
> install bioruby /System/Library/Frameworks/Ruby.framework/Versions/ 
> 1.8/usr/bin/
> install br_biofetch.rb /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/bin/
> install br_bioflat.rb /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/bin/
> install br_biogetseq.rb /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/bin/
> install br_pmfetch.rb /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/bin/
> <--- bin
> ---> lib
> mkdir -p /
> install bio.rb /
> ---> lib/bio
> mkdir -p /bio
>
> [...] (continue)
>
>
> ARGH!!!! after the bin install the install.rb install ALL the bio  
> library in ROOT!
>
> So to summarize:
>
> - first bin are install correctly in /System/Library/.../usr/bin
> - the ENTIRE library is installed in the wrong PATH (/)
>
> Please notice that in another MAC with 10.5 really similar BUT with  
> a manual installed version of ruby 1.8.7 in /url/local/bin the  
> installation of bioruby is correct and all is installed in the  
> correct path (in that case /usr/local/lib)
>
> To conclude seems that there is a BUG in install.rb that is unable  
> to install the bioruby library in /System/Library/Frameworks/ 
> Ruby.framework/Version/1.8/usr/lib
>
> If you don't have a MAC for testing, I can try to fix this, just  
> give me some clues.
>
> I have tried to specify the prefix with:
>
> ruby install.rb setup --prefix=/System/Library/Frameworks/ 
> Ruby.framework/Versions/1.8/usr
>
> but in installation I have the same problem that is summarized by  
> this 2 lines of the install log!:
>
> mkdir -p /
> install bio.rb /
>
>
> Again I can help you fix this, cause I have the right MAC to make  
> tests, but I have no clues of where is the bug....
>
>
> Best Regards
>
>
> Davide Rambaldi, Bioinformatics PhD student.
> -----------------------------------------------------
> Bioinformatic Group IFOM-IEO Campus
> Via Adamello 16, Milano
> I-20139 Italy
> [t] +39 02574303 066
> [e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it 
> >
> [i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi  
> <%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/ 
> DavideRambaldi> (homepage)
> [i] http://www.semm.it <http://www.semm.it/>             (PhD school)
> [i] http://www.btbs.unimib.it/     (Master)
> -----------------------------------------------------
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

Davide Rambaldi, Bioinformatics PhD student.
-----------------------------------------------------
Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy
[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it 
 >
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi < 
%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi>  
(homepage)
[i] http://www.semm.it <http://www.semm.it/>             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)
-----------------------------------------------------


From tomoakin at kenroku.kanazawa-u.ac.jp  Mon Oct 13 10:32:07 2008
From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA)
Date: Mon, 13 Oct 2008 23:32:07 +0900
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <9A8CA4BF-5DEE-402A-9A89-E266F139F0F9@ifom-ieo-campus.it>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<992DF6FE-14DF-45B9-B141-224FF473E82B@hgc.jp>
	<6B068F99-56FA-4E7E-AB60-887B83480F05@ifom-ieo-campus.it>
	<20080926133733.A99061CBC3F0@idnmail.gen-info.osaka-u.ac.jp>
	<9A8CA4BF-5DEE-402A-9A89-E266F139F0F9@ifom-ieo-campus.it>
Message-ID: <00B75F08-1B4E-45EE-A2E1-C873072A7F64@kenroku.kanazawa-u.ac.jp>

Hi,

> - For the database I have used the general db "sequences", assuming  
> that the method getent of entry.rb is only for sequences... is this  
> correct?


There are getseq and getent:
My feeling is that both the databases and libraries are growing
to handles datatypes other than sequences,
though the sequences have been the primary interest.
So, I would assume getent might be used in more general purpose than  
getting "sequences".

I suppose that having a database with possible db parameter string and
remote db and rettype combination is a extensible way to resolve the  
need for possible different
datatypes.
knowndbparams={"gb" => {"db" => sequences, "rettype" =>"gbwithparts"},
  "gp" => {"db" => sequences, "rettype" => "gp"},
...
}

and call like
fetch = Bio::NCBI::REST.efetch(entry_id, knwondbparams[db])

Note that with "rettype" =>"gb", large scaffolds that are composed of
several different contigs are obtained as a list of the individual
contig and without the actual sequence. This is good for the response  
time,
and the network load when the sequence part is not necessary,
but sometimes unexpected for the user.  Until it becomes to possible
to fetch the underlying sequence upon the access to the sequence of the
entry, "gbwithparts" seems the parameter to use as default.
-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan



From davide.rambaldi at ifom-ieo-campus.it  Mon Oct 13 12:05:06 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Mon, 13 Oct 2008 18:05:06 +0200
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <00B75F08-1B4E-45EE-A2E1-C873072A7F64@kenroku.kanazawa-u.ac.jp>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<992DF6FE-14DF-45B9-B141-224FF473E82B@hgc.jp>
	<6B068F99-56FA-4E7E-AB60-887B83480F05@ifom-ieo-campus.it>
	<20080926133733.A99061CBC3F0@idnmail.gen-info.osaka-u.ac.jp>
	<9A8CA4BF-5DEE-402A-9A89-E266F139F0F9@ifom-ieo-campus.it>
	<00B75F08-1B4E-45EE-A2E1-C873072A7F64@kenroku.kanazawa-u.ac.jp>
Message-ID: <E4D48C1F-1770-45DB-89CF-114B3224E8F0@ifom-ieo-campus.it>

>
>
> There are getseq and getent:
> My feeling is that both the databases and libraries are growing
> to handles datatypes other than sequences,
> though the sequences have been the primary interest.
> So, I would assume getent might be used in more general purpose than  
> getting "sequences".
>
> I suppose that having a database with possible db parameter string and
> remote db and rettype combination is a extensible way to resolve the  
> need for possible different
> datatypes.
> knowndbparams={"gb" => {"db" => sequences, "rettype" =>"gbwithparts"},
> "gp" => {"db" => sequences, "rettype" => "gp"},
> ...
> }
>
> and call like
> fetch = Bio::NCBI::REST.efetch(entry_id, knwondbparams[db])
>

I have modified to patch (see below), including a knowndbparams Hash.

Now work with:

bioruby> test = getobj("gb:AAF63163")
bioruby> test = getobj("gp:AF237819")


Actually the Hash handle genbank and genPept.

How I can add more datatypes?

I should take the definition in  NSIDs (lib/bio/io/dbget.rb) as key  
for knowdbparams Hash?

Here is (from NCBI website) the list of available db params for efetch:

1. EFETCH for literature
    db=[pubmed|pmc|journals|omim]

2. EFETCH for sequences
    	? gene
	? genome
	? nucleotide
	? nuccore
	? nucest
	? nucgss
	? protein
	? popset
	? snp
	? sequences - Composite name including nucleotide, protein, popset  
and genome.

3. EFETCH for taxonomy
    db=taxonomy


Best Regards

Davide

-------------------------------------------------------
PATCH HERE
----------------------------------------------------

Oni:bioruby tucano$ git diff
diff --git a/lib/bio.rb b/lib/bio.rb
index b2b6f4f..bddc221 100644
--- a/lib/bio.rb
+++ b/lib/bio.rb
@@ -170,6 +170,7 @@ module Bio

    class NCBI
      autoload :SOAP,       'bio/io/ncbisoap'
+    autoload :REST,       'bio/io/ncbirest'
    end


diff --git a/lib/bio/shell/plugin/entry.rb b/lib/bio/shell/plugin/ 
entry.rb
index 6d36fb5..2408a95 100644
--- a/lib/bio/shell/plugin/entry.rb
+++ b/lib/bio/shell/plugin/entry.rb
@@ -88,8 +88,19 @@ module Bio::Shell

        # KEGG API at http://www.genome.jp/kegg/soap/
        else
-        puts "Retrieving entry from KEGG API (#{arg})"
          entry = bget(arg)
+        if entry.length != 0 then
+          puts "Retrieving entry from KEGG API (#{arg})"
+        else
+          # NCBI efecth
+          knowndbparams = {
+            "gb" => {"db" => "sequences", "rettype" =>"gbwithparts"},
+            "gp" => {"db" => "sequences", "rettype" => "gp"}
+          }
+          puts "Retrieving entry from NCBI (#{arg})"
+          fetch = Bio::NCBI::REST.efetch(entry_id, knowndbparams[db])
+          entry = fetch.to_s
+        end
        end
      end




From andersbj at binf.ku.dk  Mon Oct 13 15:25:16 2008
From: andersbj at binf.ku.dk (Anders Jacobsen)
Date: Mon, 13 Oct 2008 21:25:16 +0200
Subject: [BioRuby] Biased Bio::Sequence randomize()
Message-ID: <000701c92d69$6dba9450$492fbcf0$@ku.dk>

Hi,

 

I believe that the current sequence randomization/shuffle method is severely
biased, infrequent bases are more likely to occur in the end of the sequence
than in the beginning:

 

class Array

  #returns a histogram represented as a hash

  def hist()

    h = Hash.new(0)

    self.each{|x| h[x] += 1}

    h

  end

end

 

>> (1..1000).to_a.map{|i|
Bio::Sequence::NA.new("ccccggac").randomize.index("a") + 1}.hist.sort

=> [[1, 36], [2, 51], [3, 62], [4, 97], [5, 127], [6, 189], [7, 219], [8,
219]]

 

I suggest implementing this method using the unbiased Fisher-Yates shuffle
(http://en.wikipedia.org/wiki/Fisher-Yates_shuffle)

 

class Array

  def shuffle()

    arr = self.dup

    arr.size.downto 2 do |j|

      r = Kernel::rand(j)

      arr[j-1], arr[r] = arr[r], arr[j-1]

    end

    arr

  end

end

 

(1..1000).to_a.map{|i|
Bio::Sequence::NA.new("ccccggac").split("").shuffle.index("a") +
1}.hist.sort

=> [[1, 121], [2, 127], [3, 135], [4, 119], [5, 145], [6, 104], [7, 126],
[8, 123]]

 

-Anders Jacobsen


From ktym at hgc.jp  Mon Oct 13 16:55:41 2008
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Tue, 14 Oct 2008 05:55:41 +0900
Subject: [BioRuby] Biased Bio::Sequence randomize()
In-Reply-To: <000701c92d69$6dba9450$492fbcf0$@ku.dk>
References: <000701c92d69$6dba9450$492fbcf0$@ku.dk>
Message-ID: <690F001A-C72C-4BF2-8056-E811D0431EAA@hgc.jp>

Dear Jacobsen,

> I believe that the current sequence randomization/shuffle method is severely
> biased, infrequent bases are more likely to occur in the end of the sequence
> than in the beginning:

You are right. 

I had fixed a while ago, but it seems that I forgot to commit to the repository, sorry.

Could you try the following replacement?

  def randomize(hash = nil)
    if hash
      tmp = ''
      hash.each {|k, v|
        tmp += k * v.to_i
      }
    else
      tmp = self
    end
    len = tmp.length - 1
    seq = ''
    ary = (0..len).to_a.sort_by{rand}
    ary.each do |idx|
      if block_given?
        yield tmp[idx]
      else
        seq << tmp[idx]
      end
    end
    return self.class.new(seq)
  end

I haven't yet prepared my git environment, so I hope someone (Goto-san?) can
take care of the following patch.

Regards,
Toshiaki Katayama


% cvs diff -u lib/bio/sequence/common.rb
===========================================
 dev.open-bio.org - Authorized Access Only
===========================================
Index: lib/bio/sequence/common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/common.rb,v
retrieving revision 1.6
diff -u -r1.6 common.rb
--- lib/bio/sequence/common.rb	27 Dec 2007 17:36:02 -0000	1.6
+++ lib/bio/sequence/common.rb	13 Oct 2008 20:50:27 -0000
@@ -241,28 +241,22 @@
   # * (optional) _hash_: Hash object
   # *Returns*:: new Bio::Sequence::NA/AA object
   def randomize(hash = nil)
-    length = self.length
     if hash
-      length = 0
-      count = hash.clone
-      count.each_value {|x| length += x}
+      tmp = ''
+      hash.each {|k, v|
+        tmp += k * v.to_i
+      }
     else
-      count = self.composition
+      tmp = self
     end
-
+    len = tmp.length - 1
     seq = ''
-    tmp = {}
-    length.times do 
-      count.each do |k, v|
-        tmp[k] = v * rand
-      end
-      max = tmp.max {|a, b| a[1] <=> b[1]}
-      count[max.first] -= 1
-
+    ary = (0..len).to_a.sort_by{rand}
+    ary.each do |idx|
       if block_given?
-        yield max.first
+        yield tmp[idx]
       else
-        seq += max.first
+        seq << tmp[idx]
       end
     end
     return self.class.new(seq)



On 2008/10/14, at 4:25, Anders Jacobsen wrote:

> Hi,
>
>
>
> I believe that the current sequence randomization/shuffle method is severely
> biased, infrequent bases are more likely to occur in the end of the sequence
> than in the beginning:
>
>
>
> class Array
>
>  #returns a histogram represented as a hash
>
>  def hist()
>
>    h = Hash.new(0)
>
>    self.each{|x| h[x] += 1}
>
>    h
>
>  end
>
> end
>
>
>
>>> (1..1000).to_a.map{|i|
> Bio::Sequence::NA.new("ccccggac").randomize.index("a") + 1}.hist.sort
>
> => [[1, 36], [2, 51], [3, 62], [4, 97], [5, 127], [6, 189], [7, 219], [8,
> 219]]
>
>
>
> I suggest implementing this method using the unbiased Fisher-Yates shuffle
> (http://en.wikipedia.org/wiki/Fisher-Yates_shuffle)
>
>
>
> class Array
>
>  def shuffle()
>
>    arr = self.dup
>
>    arr.size.downto 2 do |j|
>
>      r = Kernel::rand(j)
>
>      arr[j-1], arr[r] = arr[r], arr[j-1]
>
>    end
>
>    arr
>
>  end
>
> end
>
>
>
> (1..1000).to_a.map{|i|
> Bio::Sequence::NA.new("ccccggac").split("").shuffle.index("a") +
> 1}.hist.sort
>
> => [[1, 121], [2, 127], [3, 135], [4, 119], [5, 145], [6, 104], [7, 126],
> [8, 123]]
>
>
>
> -Anders Jacobsen
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From donttrustben at gmail.com  Tue Oct 14 00:51:40 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Tue, 14 Oct 2008 15:51:40 +1100
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <20081011075440.GA19106@thebird.nl>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
	<bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
	<20081011075440.GA19106@thebird.nl>
Message-ID: <bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>

Thanks for the encouragement. I've made an initial attempt at integrating
URL generation into BioRuby. I've made it available as my 'url' branch,
which is available at

http://github.com/wwood/bioruby/tree/url

Is this what you had in mind or am I misunderstanding you?

Thanks,
ben

2008/10/11 Pjotr Prins <pjotr2008 at thebird.nl>

> We could have a mixin module with methods that generate all different
> URLs in a central location. I think that is a good idea.
>
> Pj.
>
> On Sat, Oct 11, 2008 at 09:28:47AM +1100, Ben Woodcroft wrote:
> > Thanks for your response. I would have thought the fact that they change
> is
> > more reason to include it - not less.
> >
> > Is that database you speak of freely available? Just as part of the AceDB
> > download?
> >
> > Thanks,
> > ben
> >
> > 2008/10/10 Michael Han <mh6 at sanger.ac.uk>
> >
> > >
> > > On 10 Oct 2008, at 05:18, Ben Woodcroft wrote:
> > >
> > > Hi list,
> > >
> > > A common thing I find myself doing is to 'linkout' to other databases.
> For
> > > instance, I have a PDB id and I want to link to the corresponding
> record in
> > > pdb.org. Right now, I would have to go to the pdb site and try to
> reverse
> > > engineer it. In the past I've even had to email the webmasters for more
> > > information. It seems to me this is a duplication of effort, and so
> > > class(es) to collect this information for me might have a place in
> BioRuby.
> > >
> > > Does this sound reasonable to anyone? Is there any precendents out
> there?
> > > What might be a good way to structure the code?
> > >
> > > Thanks,
> > > ben
> > >
> > > --
> > > FYI: My email addresses at unimelb, uq and gmail all redirect to the
> same
> > > place.
> > > _______________________________________________
> > > BioRuby mailing list
> > > BioRuby at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioruby
> > >
> > >
> > > Hi Ben,
> > >
> > > what we did is save URL constructors in an database object in a sprintf
> > > style, which is in turn used by the xref objects linked to
> > > genes/proteins/etc.
> > > Anyway I am not sure if it is a good idea to put it in the bioruby
> library,
> > > as when you have a couple of dozens of different database, you can be
> sure
> > > that one URL will change every few days/weeks, so it is a hassle to
> keep all
> > > of them up-to-date.
> > > Michael
> > > ---------------------------------------
> > >   oo Wormbase Group, Sanger Institute
> > >   |  The Wellcome Trust Genome Campus,
> > >   |  Hinxton, Cambridge, CB10 1HH, UK.
> > >   |  Tel.: +44 (0)1223 49 6869
> > > --'
> > >
> > >
> > >
> > >
> > > -- The Wellcome Trust Sanger Institute is operated by Genome Research
> > > Limited, a charity registered in England with number 1021457 and a
> company
> > > registered in England with number 2742969, whose registered office is
> 215
> > > Euston Road, London, NW1 2BE.
> > >
> >
> >
> >
> > --
> > FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> > place.
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>



-- 
FYI: My email addresses at unimelb, uq and gmail all redirect to the same
place.

From adamnkraut at gmail.com  Tue Oct 14 11:04:23 2008
From: adamnkraut at gmail.com (Adam Kraut)
Date: Tue, 14 Oct 2008 11:04:23 -0400
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
	<bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
	<20081011075440.GA19106@thebird.nl>
	<bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>
Message-ID: <134ede0b0810140804m7fbd6005xf07ebbcef34a2529@mail.gmail.com>

I typically put these in Rails/Merb helpers.  I extracted a few from one of
my apps.  I'm still not sure if these belong in bioruby due to the huge
number of resources and urls.  I also think they're somewhat
project-specific.  You're welcome to include or modify these:

    def pdb_url_for(pdbId)
      "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#{pdbId}<http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#%7BpdbId%7D>
"
    end

    def pdbsum_url_for(pdbId)
      "
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#{pdbId}<http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#%7BpdbId%7D>
"
    end

    def cath_url_for(pdbId)
      "
http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#{pdbId}&type=PDB<http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#%7BpdbId%7D&type=PDB>
"
    end

    def scop_url_for(pdbId)
      "http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#{pdbId}<http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#%7BpdbId%7D>
"
    end

-Adam

From ktym at hgc.jp  Tue Oct 14 13:35:38 2008
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Wed, 15 Oct 2008 02:35:38 +0900
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <E4D48C1F-1770-45DB-89CF-114B3224E8F0@ifom-ieo-campus.it>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<992DF6FE-14DF-45B9-B141-224FF473E82B@hgc.jp>
	<6B068F99-56FA-4E7E-AB60-887B83480F05@ifom-ieo-campus.it>
	<20080926133733.A99061CBC3F0@idnmail.gen-info.osaka-u.ac.jp>
	<9A8CA4BF-5DEE-402A-9A89-E266F139F0F9@ifom-ieo-campus.it>
	<00B75F08-1B4E-45EE-A2E1-C873072A7F64@kenroku.kanazawa-u.ac.jp>
	<E4D48C1F-1770-45DB-89CF-114B3224E8F0@ifom-ieo-campus.it>
Message-ID: <020B141F-EC67-4FC5-A1EF-EF5C3F19638E@hgc.jp>

Hi,

I also forgot to commit my change to ncbirest.rb for TogoWS (http://togows.dbcls.jp/).
I'll attach my current version (Apr 18) and I hope some of you can take a look on it.

Regards,
Toshiaki Katayama

-------------- next part --------------




On 2008/10/14, at 1:05, Davide Rambaldi wrote:

>>
>>
>> There are getseq and getent:
>> My feeling is that both the databases and libraries are growing
>> to handles datatypes other than sequences,
>> though the sequences have been the primary interest.
>> So, I would assume getent might be used in more general purpose than getting "sequences".
>>
>> I suppose that having a database with possible db parameter string and
>> remote db and rettype combination is a extensible way to resolve the need for possible different
>> datatypes.
>> knowndbparams={"gb" => {"db" => sequences, "rettype" =>"gbwithparts"},
>> "gp" => {"db" => sequences, "rettype" => "gp"},
>> ...
>> }
>>
>> and call like
>> fetch = Bio::NCBI::REST.efetch(entry_id, knwondbparams[db])
>>
>
> I have modified to patch (see below), including a knowndbparams Hash.
>
> Now work with:
>
> bioruby> test = getobj("gb:AAF63163")
> bioruby> test = getobj("gp:AF237819")
>
>
> Actually the Hash handle genbank and genPept.
>
> How I can add more datatypes?
>
> I should take the definition in  NSIDs (lib/bio/io/dbget.rb) as key for knowdbparams Hash?
>
> Here is (from NCBI website) the list of available db params for efetch:
>
> 1. EFETCH for literature
>  db=[pubmed|pmc|journals|omim]
>
> 2. EFETCH for sequences
>  	? gene
> 	? genome
> 	? nucleotide
> 	? nuccore
> 	? nucest
> 	? nucgss
> 	? protein
> 	? popset
> 	? snp
> 	? sequences - Composite name including nucleotide, protein, popset and genome.
>
> 3. EFETCH for taxonomy
>  db=taxonomy
>
>
> Best Regards
>
> Davide
>
> -------------------------------------------------------
> PATCH HERE
> ----------------------------------------------------
>
> Oni:bioruby tucano$ git diff
> diff --git a/lib/bio.rb b/lib/bio.rb
> index b2b6f4f..bddc221 100644
> --- a/lib/bio.rb
> +++ b/lib/bio.rb
> @@ -170,6 +170,7 @@ module Bio
>
>  class NCBI
>    autoload :SOAP,       'bio/io/ncbisoap'
> +    autoload :REST,       'bio/io/ncbirest'
>  end
>
>
> diff --git a/lib/bio/shell/plugin/entry.rb b/lib/bio/shell/plugin/entry.rb
> index 6d36fb5..2408a95 100644
> --- a/lib/bio/shell/plugin/entry.rb
> +++ b/lib/bio/shell/plugin/entry.rb
> @@ -88,8 +88,19 @@ module Bio::Shell
>
>      # KEGG API at http://www.genome.jp/kegg/soap/
>      else
> -        puts "Retrieving entry from KEGG API (#{arg})"
>        entry = bget(arg)
> +        if entry.length != 0 then
> +          puts "Retrieving entry from KEGG API (#{arg})"
> +        else
> +          # NCBI efecth
> +          knowndbparams = {
> +            "gb" => {"db" => "sequences", "rettype" =>"gbwithparts"},
> +            "gp" => {"db" => "sequences", "rettype" => "gp"}
> +          }
> +          puts "Retrieving entry from NCBI (#{arg})"
> +          fetch = Bio::NCBI::REST.efetch(entry_id, knowndbparams[db])
> +          entry = fetch.to_s
> +        end
>      end
>    end
>
>
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From pjotr2008 at thebird.nl  Tue Oct 14 13:47:13 2008
From: pjotr2008 at thebird.nl (Pjotr Prins)
Date: Tue, 14 Oct 2008 19:47:13 +0200
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
	<bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
	<20081011075440.GA19106@thebird.nl>
	<bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>
Message-ID: <20081014174713.GA16130@thebird.nl>

Looks fine to me, I can add URLs for NCBI GEO access - Naohisa, what 
do you think?

Pj.

On Tue, Oct 14, 2008 at 03:51:40PM +1100, Ben Woodcroft wrote:
> Thanks for the encouragement. I've made an initial attempt at integrating
> URL generation into BioRuby. I've made it available as my 'url' branch,
> which is available at
> 
> http://github.com/wwood/bioruby/tree/url
> 
> Is this what you had in mind or am I misunderstanding you?
> 
> Thanks,
> ben
> 
> 2008/10/11 Pjotr Prins <pjotr2008 at thebird.nl>
> 
> > We could have a mixin module with methods that generate all different
> > URLs in a central location. I think that is a good idea.
> >
> > Pj.
> >
> > On Sat, Oct 11, 2008 at 09:28:47AM +1100, Ben Woodcroft wrote:
> > > Thanks for your response. I would have thought the fact that they change
> > is
> > > more reason to include it - not less.
> > >
> > > Is that database you speak of freely available? Just as part of the AceDB
> > > download?
> > >
> > > Thanks,
> > > ben
> > >
> > > 2008/10/10 Michael Han <mh6 at sanger.ac.uk>
> > >
> > > >
> > > > On 10 Oct 2008, at 05:18, Ben Woodcroft wrote:
> > > >
> > > > Hi list,
> > > >
> > > > A common thing I find myself doing is to 'linkout' to other databases.
> > For
> > > > instance, I have a PDB id and I want to link to the corresponding
> > record in
> > > > pdb.org. Right now, I would have to go to the pdb site and try to
> > reverse
> > > > engineer it. In the past I've even had to email the webmasters for more
> > > > information. It seems to me this is a duplication of effort, and so
> > > > class(es) to collect this information for me might have a place in
> > BioRuby.
> > > >
> > > > Does this sound reasonable to anyone? Is there any precendents out
> > there?
> > > > What might be a good way to structure the code?
> > > >
> > > > Thanks,
> > > > ben
> > > >
> > > > --
> > > > FYI: My email addresses at unimelb, uq and gmail all redirect to the
> > same
> > > > place.
> > > > _______________________________________________
> > > > BioRuby mailing list
> > > > BioRuby at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/bioruby
> > > >
> > > >
> > > > Hi Ben,
> > > >
> > > > what we did is save URL constructors in an database object in a sprintf
> > > > style, which is in turn used by the xref objects linked to
> > > > genes/proteins/etc.
> > > > Anyway I am not sure if it is a good idea to put it in the bioruby
> > library,
> > > > as when you have a couple of dozens of different database, you can be
> > sure
> > > > that one URL will change every few days/weeks, so it is a hassle to
> > keep all
> > > > of them up-to-date.
> > > > Michael
> > > > ---------------------------------------
> > > >   oo Wormbase Group, Sanger Institute
> > > >   |  The Wellcome Trust Genome Campus,
> > > >   |  Hinxton, Cambridge, CB10 1HH, UK.
> > > >   |  Tel.: +44 (0)1223 49 6869
> > > > --'
> > > >
> > > >
> > > >
> > > >
> > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research
> > > > Limited, a charity registered in England with number 1021457 and a
> > company
> > > > registered in England with number 2742969, whose registered office is
> > 215
> > > > Euston Road, London, NW1 2BE.
> > > >
> > >
> > >
> > >
> > > --
> > > FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> > > place.
> > > _______________________________________________
> > > BioRuby mailing list
> > > BioRuby at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> 
> 
> 
> -- 
> FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> place.

From donttrustben at gmail.com  Tue Oct 14 21:07:59 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Wed, 15 Oct 2008 12:07:59 +1100
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <134ede0b0810140804m7fbd6005xf07ebbcef34a2529@mail.gmail.com>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
	<bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
	<20081011075440.GA19106@thebird.nl>
	<bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>
	<134ede0b0810140804m7fbd6005xf07ebbcef34a2529@mail.gmail.com>
Message-ID: <bb2b67d00810141807t7547ff45kec9f62b8d802643d@mail.gmail.com>

Thanks Adam - I have included these into the module.

2008/10/15 Adam Kraut <adamnkraut at gmail.com>

> I typically put these in Rails/Merb helpers.  I extracted a few from one of
> my apps.  I'm still not sure if these belong in bioruby due to the huge
> number of resources and urls.  I also think they're somewhat
> project-specific.  You're welcome to include or modify these:
>
>     def pdb_url_for(pdbId)
>       "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#{pdbId}<http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#%7BpdbId%7D>
> "
>     end
>
>     def pdbsum_url_for(pdbId)
>       "
> http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#{pdbId}<http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#%7BpdbId%7D>
> "
>     end
>
>     def cath_url_for(pdbId)
>       "
> http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#{pdbId}&type=PDB<http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#%7BpdbId%7D&type=PDB>
> "
>     end
>
>     def scop_url_for(pdbId)
>       "http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#{pdbId}<http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#%7BpdbId%7D>
> "
>     end
>
> -Adam
>



-- 
FYI: My email addresses at unimelb, uq and gmail all redirect to the same
place.

From davide.rambaldi at ifom-ieo-campus.it  Wed Oct 15 06:26:44 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Wed, 15 Oct 2008 12:26:44 +0200
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
Message-ID: <AE11B0D0-8AB8-4B28-959B-7A5942B1FD45@ifom-ieo-campus.it>

About the installation of bioruby on a fresh MAC 10.5

I manage to install it in the correct path without install ruby in / 
usr/local/bin

Here is the story:

- I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/ 
   (setup-3.41.tar.gz)

- I just copy setup.rb in the bioruby directory (I still doesn't  
understand who generate install.rb for bioruby, is autogenerated I  
see, but with which ruby package?)

- I use the setup.rb file:

    * ruby setup.rb config
    * ruby setup.rb setup

At this point this is the config I have:

ruby setup.rb show

prefix               /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr
bindir               $prefix/bin
libdir               $prefix/lib
datadir              $prefix/share
mandir               /usr/share/man
sysconfdir           $prefix/etc
localstatedir        $prefix/var
libruby              /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/lib/ruby
librubyver           /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/lib/ruby/1.8
librubyverarch       /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0
siteruby             /Library/Ruby/Site
siterubyver          /Library/Ruby/Site/1.8
siterubyverarch      /Library/Ruby/Site/1.8/universal-darwin9.0
rbdir                $siterubyver
sodir                $siterubyverarch
rubypath             /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/ruby
rubyprog             /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/ruby
makeprog             make
shebang              ruby
without-ext          no



That compared with the config saved by install.rb is really different  
(the critical point id the siteruby path, that is in /Library/Ruby...):

ruby install.rb show
prefix     /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
std-ruby   $prefix/lib/ruby/1.8
site-ruby-common (not specified)
site-ruby  (not specified)
bin-dir    $prefix/bin
rb-dir     $site-ruby
so-dir     (not specified)
data-dir   $prefix/share
ruby-path  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
bin/ruby
ruby-prog  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
bin/ruby
make-prog  make
without-ext no



Now I can run sudo ruby setup.rb install  (or ruby setup.rb install -- 
no-harm for just checking):

And the installation goes more or less well:

- all the lib files are installed into /Library/Ruby/Site/1.8

- the binary are installed in /System/Library/Frameworks/ 
Ruby.framework/Versions/1.8/usr/bin

So remains to do a post-install command to generate a link from / 
System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/bioruby  
to /usrbin/bioruby ....


END of the story.....


I will compile my personal ruby in /usr/local/bin amd renstall bioruby  
in any case: I have seen problems also with the rubygem update,  
etc....  :-(




Davide Rambaldi, Bioinformatics PhD student.
-----------------------------------------------------
Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy
[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it 
 >
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi < 
%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi>  
(homepage)
[i] http://www.semm.it <http://www.semm.it/>             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)
-----------------------------------------------------


From ktym at hgc.jp  Wed Oct 15 20:49:54 2008
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Thu, 16 Oct 2008 09:49:54 +0900
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
In-Reply-To: <AE11B0D0-8AB8-4B28-959B-7A5942B1FD45@ifom-ieo-campus.it>
References: <AE11B0D0-8AB8-4B28-959B-7A5942B1FD45@ifom-ieo-campus.it>
Message-ID: <5FC914E6-9F4A-4AEF-BF89-C0CDB603242D@hgc.jp>

Hi,

> - I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/  (setup-3.41.tar.gz)
>
> - I just copy setup.rb in the bioruby directory (I still doesn't understand who generate install.rb for bioruby, is autogenerated I see, but with which ruby package?)

install.rb in the BioRuby package is a old version of the setup (3.1.4)
>From your experiment, we should update it to the version 3.41. Thanks!

bioruby/README:
--------------------------------------------------
== LICENSE

BioRuby can be freely distributed under the same terms as Ruby.

Note that, install.rb included in the BioRuby package comes from
setup[http://raa.ruby-lang.org/project/setup/] developed by Minero Aoki,
and modified by Moses Hohman.
--------------------------------------------------

bioruby/ChangeLog:
--------------------------------------------------
2004-12-13  KATAYAMA Toshiaki <k at bioruby.org>

        * BioRuby 0.6.2 released.

        * test/all_tests.rb:

          Unit tests for some classes are newly incorporated by
          Moses Hohman.  You can try it by 'ruby install.rb test'

2003-06-25  KATAYAMA Toshiaki  <k at bioruby.org>

        * BioRuby version 0.5.0 released.

        * install.rb:

            Changed to use setup 3.1.4 to avoid installing CVS/ directory.
--------------------------------------------------

Regards,
Toshiaki Katayama


On 2008/10/15, at 19:26, Davide Rambaldi wrote:

> About the installation of bioruby on a fresh MAC 10.5
>
> I manage to install it in the correct path without install ruby in /usr/local/bin
>
> Here is the story:
>
> - I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/  (setup-3.41.tar.gz)
>
> - I just copy setup.rb in the bioruby directory (I still doesn't understand who generate install.rb for bioruby, is autogenerated I see, but with which ruby package?)
>
> - I use the setup.rb file:
>
>   * ruby setup.rb config
>   * ruby setup.rb setup
>
> At this point this is the config I have:
>
> ruby setup.rb show
>
> prefix               /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> bindir               $prefix/bin
> libdir               $prefix/lib
> datadir              $prefix/share
> mandir               /usr/share/man
> sysconfdir           $prefix/etc
> localstatedir        $prefix/var
> libruby              /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby
> librubyver           /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8
> librubyverarch       /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0
> siteruby             /Library/Ruby/Site
> siterubyver          /Library/Ruby/Site/1.8
> siterubyverarch      /Library/Ruby/Site/1.8/universal-darwin9.0
> rbdir                $siterubyver
> sodir                $siterubyverarch
> rubypath             /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> rubyprog             /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> makeprog             make
> shebang              ruby
> without-ext          no
>
>
>
> That compared with the config saved by install.rb is really different (the critical point id the siteruby path, that is in /Library/Ruby...):
>
> ruby install.rb show
> prefix     /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> std-ruby   $prefix/lib/ruby/1.8
> site-ruby-common (not specified)
> site-ruby  (not specified)
> bin-dir    $prefix/bin
> rb-dir     $site-ruby
> so-dir     (not specified)
> data-dir   $prefix/share
> ruby-path  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> ruby-prog  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> make-prog  make
> without-ext no
>
>
>
> Now I can run sudo ruby setup.rb install  (or ruby setup.rb install --no-harm for just checking):
>
> And the installation goes more or less well:
>
> - all the lib files are installed into /Library/Ruby/Site/1.8
>
> - the binary are installed in /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin
>
> So remains to do a post-install command to generate a link from /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/bioruby to /usrbin/bioruby ....
>
>
> END of the story.....
>
>
> I will compile my personal ruby in /usr/local/bin amd renstall bioruby in any case: I have seen problems also with the rubygem update, etc....  :-(
>
>
>
>
> Davide Rambaldi, Bioinformatics PhD student.
> -----------------------------------------------------
> Bioinformatic Group IFOM-IEO Campus
> Via Adamello 16, Milano
> I-20139 Italy
> [t] +39 02574303 066
> [e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it>
> [i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi <%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi> (homepage)
> [i] http://www.semm.it <http://www.semm.it/>             (PhD school)
> [i] http://www.btbs.unimib.it/     (Master)
> -----------------------------------------------------
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby




From ngoto at gen-info.osaka-u.ac.jp  Fri Oct 17 11:10:38 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 18 Oct 2008 00:10:38 +0900
Subject: [BioRuby] Biased Bio::Sequence randomize()
In-Reply-To: <690F001A-C72C-4BF2-8056-E811D0431EAA@hgc.jp>
References: <000701c92d69$6dba9450$492fbcf0$@ku.dk>
	<690F001A-C72C-4BF2-8056-E811D0431EAA@hgc.jp>
Message-ID: <20081017151038.67AD41CBC400@idnmail.gen-info.osaka-u.ac.jp>

Hi,

First, I implemented unit tests for Bio::Sequence::Common,
including chi-square test of equiprobability, and fixed the bug
by using Fisher-Yates shuffle, as suggested by Anders.

http://github.com/bioruby/bioruby/commit/02de70cbf036b41a50d770954f3b16ba2beca880
(Sorry for typo in the commit message)

On Tue, 14 Oct 2008 05:55:41 +0900
Toshiaki Katayama <ktym at hgc.jp> wrote:

> Dear Jacobsen,
> 
> > I believe that the current sequence randomization/shuffle method is severely
> > biased, infrequent bases are more likely to occur in the end of the sequence
> > than in the beginning:
> 
> You are right. 
> 
> I had fixed a while ago, but it seems that I forgot to commit to the repository, sorry.
> 
> Could you try the following replacement?

It works fine without blocks, but when giving a block,
the bahavior is different from the original one.
In addition, "(0..len).to_a.sort_by{rand}" is too expensive
when the sequence is long. So, I changed directly modifying
duplicated sequence, and fixed the bugs, based on your code.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

From ngoto at gen-info.osaka-u.ac.jp  Sun Oct 19 01:15:10 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sun, 19 Oct 2008 14:15:10 +0900
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
In-Reply-To: <5FC914E6-9F4A-4AEF-BF89-C0CDB603242D@hgc.jp>
References: <AE11B0D0-8AB8-4B28-959B-7A5942B1FD45@ifom-ieo-campus.it>
	<5FC914E6-9F4A-4AEF-BF89-C0CDB603242D@hgc.jp>
Message-ID: <20081019051510.CEB0E1CBC4B1@idnmail.gen-info.osaka-u.ac.jp>

Hi,

I get the setup.rb from Minero Aoki's svn repository
(see http://i.loveruby.net/en/projects/setup/ for details),
and replace install.rb with this newest setup.rb.
README.rdoc is also modified.

http://github.com/bioruby/bioruby/commit/9def7df5b81340c49534ff0bb932de62402a1c8d

Thanks,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 16 Oct 2008 09:49:54 +0900
Toshiaki Katayama <ktym at hgc.jp> wrote:

> Hi,
> 
> > - I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/  (setup-3.41.tar.gz)
> >
> > - I just copy setup.rb in the bioruby directory (I still doesn't understand who generate install.rb for bioruby, is autogenerated I see, but with which ruby package?)
> 
> install.rb in the BioRuby package is a old version of the setup (3.1.4)
> >From your experiment, we should update it to the version 3.41. Thanks!
> 
> bioruby/README:
> --------------------------------------------------
> == LICENSE
> 
> BioRuby can be freely distributed under the same terms as Ruby.
> 
> Note that, install.rb included in the BioRuby package comes from
> setup[http://raa.ruby-lang.org/project/setup/] developed by Minero Aoki,
> and modified by Moses Hohman.
> --------------------------------------------------
> 
> bioruby/ChangeLog:
> --------------------------------------------------
> 2004-12-13  KATAYAMA Toshiaki <k at bioruby.org>
> 
>         * BioRuby 0.6.2 released.
> 
>         * test/all_tests.rb:
> 
>           Unit tests for some classes are newly incorporated by
>           Moses Hohman.  You can try it by 'ruby install.rb test'
> 
> 2003-06-25  KATAYAMA Toshiaki  <k at bioruby.org>
> 
>         * BioRuby version 0.5.0 released.
> 
>         * install.rb:
> 
>             Changed to use setup 3.1.4 to avoid installing CVS/ directory.
> --------------------------------------------------
> 
> Regards,
> Toshiaki Katayama
> 
> 
> On 2008/10/15, at 19:26, Davide Rambaldi wrote:
> 
> > About the installation of bioruby on a fresh MAC 10.5
> >
> > I manage to install it in the correct path without install ruby in /usr/local/bin
> >
> > Here is the story:
> >
> > - I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/  (setup-3.41.tar.gz)
> >
> > - I just copy setup.rb in the bioruby directory (I still doesn't understand who generate install.rb for bioruby, is autogenerated I see, but with which ruby package?)
> >
> > - I use the setup.rb file:
> >
> >   * ruby setup.rb config
> >   * ruby setup.rb setup
> >
> > At this point this is the config I have:
> >
> > ruby setup.rb show
> >
> > prefix               /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> > bindir               $prefix/bin
> > libdir               $prefix/lib
> > datadir              $prefix/share
> > mandir               /usr/share/man
> > sysconfdir           $prefix/etc
> > localstatedir        $prefix/var
> > libruby              /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby
> > librubyver           /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8
> > librubyverarch       /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0
> > siteruby             /Library/Ruby/Site
> > siterubyver          /Library/Ruby/Site/1.8
> > siterubyverarch      /Library/Ruby/Site/1.8/universal-darwin9.0
> > rbdir                $siterubyver
> > sodir                $siterubyverarch
> > rubypath             /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > rubyprog             /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > makeprog             make
> > shebang              ruby
> > without-ext          no
> >
> >
> >
> > That compared with the config saved by install.rb is really different (the critical point id the siteruby path, that is in /Library/Ruby...):
> >
> > ruby install.rb show
> > prefix     /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> > std-ruby   $prefix/lib/ruby/1.8
> > site-ruby-common (not specified)
> > site-ruby  (not specified)
> > bin-dir    $prefix/bin
> > rb-dir     $site-ruby
> > so-dir     (not specified)
> > data-dir   $prefix/share
> > ruby-path  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > ruby-prog  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > make-prog  make
> > without-ext no
> >
> >
> >
> > Now I can run sudo ruby setup.rb install  (or ruby setup.rb install --no-harm for just checking):
> >
> > And the installation goes more or less well:
> >
> > - all the lib files are installed into /Library/Ruby/Site/1.8
> >
> > - the binary are installed in /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin
> >
> > So remains to do a post-install command to generate a link from /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/bioruby to /usrbin/bioruby ....
> >
> >
> > END of the story.....
> >
> >
> > I will compile my personal ruby in /usr/local/bin amd renstall bioruby in any case: I have seen problems also with the rubygem update, etc....  :-(
> >
> >
> >
> >
> > Davide Rambaldi, Bioinformatics PhD student.
> > -----------------------------------------------------
> > Bioinformatic Group IFOM-IEO Campus
> > Via Adamello 16, Milano
> > I-20139 Italy
> > [t] +39 02574303 066
> > [e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it>
> > [i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi <%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi> (homepage)
> > [i] http://www.semm.it <http://www.semm.it/>             (PhD school)
> > [i] http://www.btbs.unimib.it/     (Master)
> > -----------------------------------------------------
> >
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> 
> 
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

From email2ants at gmail.com  Mon Oct 20 10:05:35 2008
From: email2ants at gmail.com (Anthony Underwood)
Date: Mon, 20 Oct 2008 15:05:35 +0100
Subject: [BioRuby] trace files (scf/abi) and ruby/bioruby
In-Reply-To: <20081003034209.939C81CBC434@idnmail.gen-info.osaka-u.ac.jp>
References: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>
	<4c7507a70810021104v7fd9c09dx57e317c2573e60a7@mail.gmail.com>
	<20081003034209.939C81CBC434@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <B866A193-D41A-49B4-8565-63F175099D80@gmail.com>

Work on the chromatogram reading classes in making good progress.  
Using a fork of the github bioruby repository I have been  
incorporating the classes into bioruby in the hope that it can be   
merged into the main bioruby repository.

However I have run into a problem with the to_biosequence method.
I have a Scf class that is a subclass of Chromatogram

Chromatogram has a method
     def to_biosequence
       Bio::Sequence.adapter(self, Bio::Sequence::Adapter::Chromatogram)
     end

I have added a line to autoload the  
Bio::Sequence::Adapter::Chromatogram module in the  
Bio::Sequence::Adapter Class.

The problem is that the to_biosequence method returns nil.

I have also found that this is the case when I test fasta and genbank  
sequences using  the existing Bio::FastaFormat and Bio::Genbank  
Classes when I use a fresh checkout of the main bioruby repository  
from github, so I don't think it's something I've done.

I see that the Bio::Sequence adapter method that to_biosequence calls  
is as follows

   def self.adapter(source_data, adapter_module)
     biosequence = self.new(nil)
     biosequence.instance_eval {
       remove_instance_variable(:@seq)
       @source_data = source_data
     }
     biosequence.extend(adapter_module)
     biosequence
   end

the last line does not return a biosequence even though if I puts  
biosequence.class just before the last line the output is Bio::Sequence.

Strangely if I insert the method call  biosequence.seq just before the  
last line of the adapter method everything is fine.

Does anybody know what's occurring here. Any help much appreciated.

Thanks

Anthony
On 3 Oct 2008, at 04:42, Naohisa GOTO wrote:

> Hi,
>
> For ABI traces, as far as I know, some person made previously,
> but all codes are lost now.
>
> http://open-bio.org/pipermail/bioruby/2005-September/000128.html
> but I cannot access to the URL described in the above archive.
>
> I don't remember why it wasn't included in bioruby, but,
> the thread of ML archive suggests that no one made any efforts
> to change the code adopting the development guideline.
>
> As Jan says, looking at bioperl, biopython, biojava, Staden, etc.
> and to write your own code seems good.
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
> On Thu, 2 Oct 2008 19:04:45 +0100
> "Jan Aerts" <jan.aerts at gmail.com> wrote:
>
>> If there's nothing there yet, you might have a look at the bioperl  
>> version
>> and take that as a guide.
>>
>> jan.
>>
>> 2008/10/2 Anthony Underwood <email2ants at gmail.com>
>>
>>> Hi all,
>>>
>>> Does anybody know if there is or someone is working on a ruby  
>>> module for
>>> reading abi/scf trace files. I was thinking of perhaps having a go  
>>> at this
>>> but thought I would check that there is no work in progress that I  
>>> should
>>> know about. I have done a few Google searches but come up with  
>>> nothing so
>>> thought I would ask on this list as well.
>>>
>>> Many thanks
>>>
>>> Anthony
>>> _______________________________________________
>>> BioRuby mailing list
>>> BioRuby at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>>
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From ngoto at gen-info.osaka-u.ac.jp  Mon Oct 20 11:21:18 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 21 Oct 2008 00:21:18 +0900
Subject: [BioRuby] trace files (scf/abi) and ruby/bioruby
In-Reply-To: <B866A193-D41A-49B4-8565-63F175099D80@gmail.com>
References: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>
	<4c7507a70810021104v7fd9c09dx57e317c2573e60a7@mail.gmail.com>
	<20081003034209.939C81CBC434@idnmail.gen-info.osaka-u.ac.jp>
	<B866A193-D41A-49B4-8565-63F175099D80@gmail.com>
Message-ID: <20081020152119.4C6611CBC3E0@idnmail.gen-info.osaka-u.ac.jp>

Thank you.

Please tell us the URL of your git repository.

Which version of Ruby do you use?
% ruby -v 

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Mon, 20 Oct 2008 15:05:35 +0100
Anthony Underwood <email2ants at gmail.com> wrote:

> Work on the chromatogram reading classes in making good progress.  
> Using a fork of the github bioruby repository I have been  
> incorporating the classes into bioruby in the hope that it can be   
> merged into the main bioruby repository.
>
> However I have run into a problem with the to_biosequence method.
> I have a Scf class that is a subclass of Chromatogram
> 
> Chromatogram has a method
>      def to_biosequence
>        Bio::Sequence.adapter(self, Bio::Sequence::Adapter::Chromatogram)
>      end
> 
> I have added a line to autoload the  
> Bio::Sequence::Adapter::Chromatogram module in the  
> Bio::Sequence::Adapter Class.
> 
> The problem is that the to_biosequence method returns nil.
> 
> I have also found that this is the case when I test fasta and genbank  
> sequences using  the existing Bio::FastaFormat and Bio::Genbank  
> Classes when I use a fresh checkout of the main bioruby repository  
> from github, so I don't think it's something I've done.
> 
> I see that the Bio::Sequence adapter method that to_biosequence calls  
> is as follows
> 
>    def self.adapter(source_data, adapter_module)
>      biosequence = self.new(nil)
>      biosequence.instance_eval {
>        remove_instance_variable(:@seq)
>        @source_data = source_data
>      }
>      biosequence.extend(adapter_module)
>      biosequence
>    end
> 
> the last line does not return a biosequence even though if I puts  
> biosequence.class just before the last line the output is Bio::Sequence.
> 
> Strangely if I insert the method call  biosequence.seq just before the  
> last line of the adapter method everything is fine.
> 
> Does anybody know what's occurring here. Any help much appreciated.
> 
> Thanks
> 
> Anthony
> On 3 Oct 2008, at 04:42, Naohisa GOTO wrote:
> 
> > Hi,
> >
> > For ABI traces, as far as I know, some person made previously,
> > but all codes are lost now.
> >
> > http://open-bio.org/pipermail/bioruby/2005-September/000128.html
> > but I cannot access to the URL described in the above archive.
> >
> > I don't remember why it wasn't included in bioruby, but,
> > the thread of ML archive suggests that no one made any efforts
> > to change the code adopting the development guideline.
> >
> > As Jan says, looking at bioperl, biopython, biojava, Staden, etc.
> > and to write your own code seems good.
> >
> > Naohisa Goto
> > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> >
> > On Thu, 2 Oct 2008 19:04:45 +0100
> > "Jan Aerts" <jan.aerts at gmail.com> wrote:
> >
> >> If there's nothing there yet, you might have a look at the bioperl  
> >> version
> >> and take that as a guide.
> >>
> >> jan.
> >>
> >> 2008/10/2 Anthony Underwood <email2ants at gmail.com>
> >>
> >>> Hi all,
> >>>
> >>> Does anybody know if there is or someone is working on a ruby  
> >>> module for
> >>> reading abi/scf trace files. I was thinking of perhaps having a go  
> >>> at this
> >>> but thought I would check that there is no work in progress that I  
> >>> should
> >>> know about. I have done a few Google searches but come up with  
> >>> nothing so
> >>> thought I would ask on this list as well.
> >>>
> >>> Many thanks
> >>>
> >>> Anthony
> >>> _______________________________________________
> >>> BioRuby mailing list
> >>> BioRuby at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioruby
> >>>
> >> _______________________________________________
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> 


From georgkam at gmail.com  Thu Oct 23 02:15:42 2008
From: georgkam at gmail.com (George Githinji)
Date: Thu, 23 Oct 2008 09:15:42 +0300
Subject: [BioRuby] can the real official bioruby site standup?
Message-ID: <55915f820810222315m1632fe8bo32849e99c5f2269a@mail.gmail.com>

Hi,
Just wondering, which is the official bioruby site?
this one
http://bioruby.open-bio.org/

or
http://www.bioruby.org/

The first one seems to be well designed and very nice,  Is it possible
for bioruby.org domain to automatically redirect to
http://bioruby.open-bio.org/

Thanks
--
---------------
Sincerely
George

Skype: george_g2
Website: http://biorelated.wordpress.com/

From mauricio at open-bio.org  Thu Oct 23 11:08:44 2008
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Thu, 23 Oct 2008 10:08:44 -0500
Subject: [BioRuby] can the real official bioruby site standup?
In-Reply-To: <55915f820810222315m1632fe8bo32849e99c5f2269a@mail.gmail.com>
References: <55915f820810222315m1632fe8bo32849e99c5f2269a@mail.gmail.com>
Message-ID: <4900937C.4040401@open-bio.org>

Hi George,

There's a pending request at the OBF Helpdesk to have this redirect set 
up, however, Toshiaki has DNS control of the bioruby.org domain and he 
would need to point it to the IP address for the bioruby.open-bio.org site.

Regards,
Mauricio.


George Githinji wrote:
> Hi,
> Just wondering, which is the official bioruby site?
> this one
> http://bioruby.open-bio.org/
> 
> or
> http://www.bioruby.org/
> 
> The first one seems to be well designed and very nice,  Is it possible
> for bioruby.org domain to automatically redirect to
> http://bioruby.open-bio.org/
> 
> Thanks
> --
> ---------------
> Sincerely
> George
> 
> Skype: george_g2
> Website: http://biorelated.wordpress.com/
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
> 

From ixpata at gmail.com  Thu Oct 23 11:15:50 2008
From: ixpata at gmail.com (Steve Mitchell)
Date: Thu, 23 Oct 2008 11:15:50 -0400
Subject: [BioRuby]  bioruby tutorials?
Message-ID: <74b8d37e0810230815j294c05f7sa3b1e669a2008a61@mail.gmail.com>

>
> Anybody know of any good bioruby tutorials? I started going through the
> wiki bioruby tutorial, but I'm pretty new and I think I need something more
> basic or maybe something with exercises that would require me to put some of
> this stuff into practice.
>

Thanks.

From jan.aerts at gmail.com  Thu Oct 23 11:25:29 2008
From: jan.aerts at gmail.com (Jan Aerts)
Date: Thu, 23 Oct 2008 16:25:29 +0100
Subject: [BioRuby] bioruby tutorials?
In-Reply-To: <74b8d37e0810230815j294c05f7sa3b1e669a2008a61@mail.gmail.com>
References: <74b8d37e0810230815j294c05f7sa3b1e669a2008a61@mail.gmail.com>
Message-ID: <4c7507a70810230825m4f047146n2f9adb00df2122e4@mail.gmail.com>

I really like the tutorials that are provided on the bio*perl* website (
http://www.bioperl.org/wiki/HOWTOs). The bioperl documentation explains how
each class works (exactly like the bioruby rdoc), but the howtos take a
problem-oriented approach. They explain how to tackle a certain problem
which might include cross-class interactions.

At the moment we don't have any of these tutorials on the website yet (there
obviously _is_ the general tutorial, but some more specific howtos would be
good) and I don't know if anyone is actually working on one. If anyone has
an idea on how to get people writing these tutorials: let us know!

jan.



2008/10/23 Steve Mitchell <ixpata at gmail.com>

> >
> > Anybody know of any good bioruby tutorials? I started going through the
> > wiki bioruby tutorial, but I'm pretty new and I think I need something
> more
> > basic or maybe something with exercises that would require me to put some
> of
> > this stuff into practice.
> >
>
> Thanks.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

From email2ants at gmail.com  Thu Oct  2 17:16:04 2008
From: email2ants at gmail.com (Anthony Underwood)
Date: Thu, 2 Oct 2008 18:16:04 +0100
Subject: [BioRuby] trace files (scf/abi) and ruby/bioruby
Message-ID: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>

Hi all,

Does anybody know if there is or someone is working on a ruby module  
for reading abi/scf trace files. I was thinking of perhaps having a go  
at this but thought I would check that there is no work in progress  
that I should know about. I have done a few Google searches but come  
up with nothing so thought I would ask on this list as well.

Many thanks

Anthony


From jan.aerts at gmail.com  Thu Oct  2 18:04:45 2008
From: jan.aerts at gmail.com (Jan Aerts)
Date: Thu, 2 Oct 2008 19:04:45 +0100
Subject: [BioRuby] trace files (scf/abi) and ruby/bioruby
In-Reply-To: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>
References: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>
Message-ID: <4c7507a70810021104v7fd9c09dx57e317c2573e60a7@mail.gmail.com>

If there's nothing there yet, you might have a look at the bioperl version
and take that as a guide.

jan.

2008/10/2 Anthony Underwood <email2ants at gmail.com>

> Hi all,
>
> Does anybody know if there is or someone is working on a ruby module for
> reading abi/scf trace files. I was thinking of perhaps having a go at this
> but thought I would check that there is no work in progress that I should
> know about. I have done a few Google searches but come up with nothing so
> thought I would ask on this list as well.
>
> Many thanks
>
> Anthony
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From ngoto at gen-info.osaka-u.ac.jp  Fri Oct  3 03:42:09 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Fri, 3 Oct 2008 12:42:09 +0900
Subject: [BioRuby] trace files (scf/abi) and ruby/bioruby
In-Reply-To: <4c7507a70810021104v7fd9c09dx57e317c2573e60a7@mail.gmail.com>
References: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>
	<4c7507a70810021104v7fd9c09dx57e317c2573e60a7@mail.gmail.com>
Message-ID: <20081003034209.939C81CBC434@idnmail.gen-info.osaka-u.ac.jp>

Hi,

For ABI traces, as far as I know, some person made previously, 
but all codes are lost now.

http://open-bio.org/pipermail/bioruby/2005-September/000128.html
but I cannot access to the URL described in the above archive.

I don't remember why it wasn't included in bioruby, but,
the thread of ML archive suggests that no one made any efforts
to change the code adopting the development guideline.

As Jan says, looking at bioperl, biopython, biojava, Staden, etc.
and to write your own code seems good.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 2 Oct 2008 19:04:45 +0100
"Jan Aerts" <jan.aerts at gmail.com> wrote:

> If there's nothing there yet, you might have a look at the bioperl version
> and take that as a guide.
> 
> jan.
> 
> 2008/10/2 Anthony Underwood <email2ants at gmail.com>
> 
> > Hi all,
> >
> > Does anybody know if there is or someone is working on a ruby module for
> > reading abi/scf trace files. I was thinking of perhaps having a go at this
> > but thought I would check that there is no work in progress that I should
> > know about. I have done a few Google searches but come up with nothing so
> > thought I would ask on this list as well.
> >
> > Many thanks
> >
> > Anthony
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From jan.aerts at gmail.com  Fri Oct  3 17:05:28 2008
From: jan.aerts at gmail.com (Jan Aerts)
Date: Fri, 3 Oct 2008 18:05:28 +0100
Subject: [BioRuby] ruby API to ensembl database
Message-ID: <4c7507a70810031005t2fa4864ct850c7769eb2b372a@mail.gmail.com>

All,

Just to let you know that we updated the Ensembl ruby API so that it also
works for version 50. There are no different APIs for each release of the
database; just mention the release number in your connection. In addition to
core, Francesco Strozzi has been working on the API for the variation
database, the first version of which is now also available.

In addition to the API itself, the latest release also contains an 'ensembl'
executable that will drop you in interactive ruby (irb) already connected to
one of the databases. Just run "ensembl homo_sapiens 50".

Development is on the github site at
http://github.com/jandot/ruby-ensembl-api. The API documentation and
tutorial are at http://www.sanger.ac.uk/Users/ja8/. To install: download the
gem from the github site and run "gem install ruby-ensembl-api-0.9.2.gem".

Small sample of script using the API:
<begin of sample>

DBConnection.connect('homo_sapiens')

slice = Slice.fetch_by_region('chromosome','4',10000,99999,-1)
slice.genes.each do |gene|
  puts gene.stable_id + "\t" + gene.status + "\t" + gene.slice.display_name
end


<end of sample>

jan.


From sebe at nmr.mpibpc.mpg.de  Tue Oct  7 07:22:00 2008
From: sebe at nmr.mpibpc.mpg.de (Sebastian Becker)
Date: Tue, 7 Oct 2008 09:22:00 +0200
Subject: [BioRuby] isoelctric point for proteins
Message-ID: <34683B72-8C2D-4C39-8856-A084F903918A@nmr.mpibpc.mpg.de>

Hi folks,

I am wondering if there is a module in BioRuby for calculating the  
iep (isoelectric point) for proteins?
I appreciate all infos.

Cheers
Sebastian


From matias.piipari at gmail.com  Tue Oct  7 14:17:02 2008
From: matias.piipari at gmail.com (Matias Piipari)
Date: Tue, 7 Oct 2008 15:17:02 +0100
Subject: [BioRuby] Querying the NCBI taxonomy with bioruby?
Message-ID: <15cdf3360810070717uee04bc8ra2ef66fe6e7f6ced@mail.gmail.com>

Is it possible to query organism names that match a given NCBI taxonomy ID
with bioruby? My API doc searches haven't uncovered anything like this for
querying the taxonomy at least, but just thought I'd check before I write it
myself.

Thanks,
Matias


From donttrustben at gmail.com  Fri Oct 10 04:18:32 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Fri, 10 Oct 2008 15:18:32 +1100
Subject: [BioRuby] URL Generation in Bioruby
Message-ID: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>

Hi list,

A common thing I find myself doing is to 'linkout' to other databases. For
instance, I have a PDB id and I want to link to the corresponding record in
pdb.org. Right now, I would have to go to the pdb site and try to reverse
engineer it. In the past I've even had to email the webmasters for more
information. It seems to me this is a duplication of effort, and so
class(es) to collect this information for me might have a place in BioRuby.

Does this sound reasonable to anyone? Is there any precendents out there?
What might be a good way to structure the code?

Thanks,
ben

-- 
FYI: My email addresses at unimelb, uq and gmail all redirect to the same
place.


From donttrustben at gmail.com  Fri Oct 10 22:28:47 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Sat, 11 Oct 2008 09:28:47 +1100
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
Message-ID: <bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>

Thanks for your response. I would have thought the fact that they change is
more reason to include it - not less.

Is that database you speak of freely available? Just as part of the AceDB
download?

Thanks,
ben

2008/10/10 Michael Han <mh6 at sanger.ac.uk>

>
> On 10 Oct 2008, at 05:18, Ben Woodcroft wrote:
>
> Hi list,
>
> A common thing I find myself doing is to 'linkout' to other databases. For
> instance, I have a PDB id and I want to link to the corresponding record in
> pdb.org. Right now, I would have to go to the pdb site and try to reverse
> engineer it. In the past I've even had to email the webmasters for more
> information. It seems to me this is a duplication of effort, and so
> class(es) to collect this information for me might have a place in BioRuby.
>
> Does this sound reasonable to anyone? Is there any precendents out there?
> What might be a good way to structure the code?
>
> Thanks,
> ben
>
> --
> FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> place.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>
>
> Hi Ben,
>
> what we did is save URL constructors in an database object in a sprintf
> style, which is in turn used by the xref objects linked to
> genes/proteins/etc.
> Anyway I am not sure if it is a good idea to put it in the bioruby library,
> as when you have a couple of dozens of different database, you can be sure
> that one URL will change every few days/weeks, so it is a hassle to keep all
> of them up-to-date.
> Michael
> ---------------------------------------
>   oo Wormbase Group, Sanger Institute
>   |  The Wellcome Trust Genome Campus,
>   |  Hinxton, Cambridge, CB10 1HH, UK.
>   |  Tel.: +44 (0)1223 49 6869
> --'
>
>
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose registered office is 215
> Euston Road, London, NW1 2BE.
>



-- 
FYI: My email addresses at unimelb, uq and gmail all redirect to the same
place.


From pjotr2008 at thebird.nl  Sat Oct 11 07:54:40 2008
From: pjotr2008 at thebird.nl (Pjotr Prins)
Date: Sat, 11 Oct 2008 09:54:40 +0200
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
	<bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
Message-ID: <20081011075440.GA19106@thebird.nl>

We could have a mixin module with methods that generate all different
URLs in a central location. I think that is a good idea.

Pj.

On Sat, Oct 11, 2008 at 09:28:47AM +1100, Ben Woodcroft wrote:
> Thanks for your response. I would have thought the fact that they change is
> more reason to include it - not less.
> 
> Is that database you speak of freely available? Just as part of the AceDB
> download?
> 
> Thanks,
> ben
> 
> 2008/10/10 Michael Han <mh6 at sanger.ac.uk>
> 
> >
> > On 10 Oct 2008, at 05:18, Ben Woodcroft wrote:
> >
> > Hi list,
> >
> > A common thing I find myself doing is to 'linkout' to other databases. For
> > instance, I have a PDB id and I want to link to the corresponding record in
> > pdb.org. Right now, I would have to go to the pdb site and try to reverse
> > engineer it. In the past I've even had to email the webmasters for more
> > information. It seems to me this is a duplication of effort, and so
> > class(es) to collect this information for me might have a place in BioRuby.
> >
> > Does this sound reasonable to anyone? Is there any precendents out there?
> > What might be a good way to structure the code?
> >
> > Thanks,
> > ben
> >
> > --
> > FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> > place.
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> >
> > Hi Ben,
> >
> > what we did is save URL constructors in an database object in a sprintf
> > style, which is in turn used by the xref objects linked to
> > genes/proteins/etc.
> > Anyway I am not sure if it is a good idea to put it in the bioruby library,
> > as when you have a couple of dozens of different database, you can be sure
> > that one URL will change every few days/weeks, so it is a hassle to keep all
> > of them up-to-date.
> > Michael
> > ---------------------------------------
> >   oo Wormbase Group, Sanger Institute
> >   |  The Wellcome Trust Genome Campus,
> >   |  Hinxton, Cambridge, CB10 1HH, UK.
> >   |  Tel.: +44 (0)1223 49 6869
> > --'
> >
> >
> >
> >
> > -- The Wellcome Trust Sanger Institute is operated by Genome Research
> > Limited, a charity registered in England with number 1021457 and a company
> > registered in England with number 2742969, whose registered office is 215
> > Euston Road, London, NW1 2BE.
> >
> 
> 
> 
> -- 
> FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> place.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From davide.rambaldi at ifom-ieo-campus.it  Sun Oct 12 15:10:14 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Sun, 12 Oct 2008 17:10:14 +0200
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <20080926133733.A99061CBC3F0@idnmail.gen-info.osaka-u.ac.jp>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<992DF6FE-14DF-45B9-B141-224FF473E82B@hgc.jp>
	<6B068F99-56FA-4E7E-AB60-887B83480F05@ifom-ieo-campus.it>
	<20080926133733.A99061CBC3F0@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <9A8CA4BF-5DEE-402A-9A89-E266F139F0F9@ifom-ieo-campus.it>


Il giorno 26/set/08, alle ore 15:37, Naohisa GOTO ha scritto:

> Thank you for a patch, but it has some problems:
> For KEGG API, $?.exitstatus has no mean, and no need to check $?.
> The "AF237819" should not be hardcoded because the method is
> not only for demo, but a bioruby-shell command to fetch entry
> specified by a user. Also note that "db" => "nuccore" would
> not always be good. (If result is empty, switching to another
> database and trying again would be the best way.)


I apologize for this.... was really stupid and sorry for the late  
answer (my laptop have died... with all my bioruby test inside)

Maybe I can propose anther patch: the patch to bio.rb add an autoload  
call for Bio::NCBI::REST in bio.rb, the patch to bio/shell/plugin/ 
entry.rb don't have the entry hardcoded.

About the entry.rb patch I have two questions:

- I put the db prefix (demo is gb:AF237819) to define the rettype for  
NCBI::REST. Work for the demo. but I guess this should be changed...

- For the database I have used the general db "sequences", assuming  
that the method getent of entry.rb is only for sequences... is this  
correct?


PATCHES:

diff --git a/lib/bio.rb b/lib/bio.rb
index b2b6f4f..bddc221 100644
--- a/lib/bio.rb
+++ b/lib/bio.rb
@@ -170,6 +170,7 @@ module Bio

    class NCBI
      autoload :SOAP,       'bio/io/ncbisoap'
+    autoload :REST,       'bio/io/ncbirest'
    end


diff --git a/lib/bio/shell/plugin/entry.rb b/lib/bio/shell/plugin/ 
entry.rb
index 6d36fb5..21ef9f6 100644
--- a/lib/bio/shell/plugin/entry.rb
+++ b/lib/bio/shell/plugin/entry.rb
@@ -88,8 +88,14 @@ module Bio::Shell

        # KEGG API at http://www.genome.jp/kegg/soap/
        else
-        puts "Retrieving entry from KEGG API (#{arg})"
          entry = bget(arg)
+        if entry.length != 0 then
+          puts "Retrieving entry from KEGG API (#{arg})"
+        else
+          puts "Retrieving entry from NCBI (#{arg})"
+          fetch = Bio::NCBI::REST.efetch(entry_id,  
{"db"=>"sequences", "rettype"=>db})
+          entry = fetch.to_s
+        end
        end
      end


Best Regards.



Davide Rambaldi,
Bioinformatics PhD student.
-----------------------------------------------------
Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy

[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi  
(homepage)
[i] http://www.semm.it             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)

-----------------------------------------------------






From davide.rambaldi at ifom-ieo-campus.it  Mon Oct 13 12:34:18 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Mon, 13 Oct 2008 14:34:18 +0200
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
Message-ID: <3D8E9D1A-CB03-46C5-B2F5-6FD46D96A4CD@ifom-ieo-campus.it>

Hi all,

the machine is an Intel Darwin 9.5.0 (MAC OSX 10.5.5), is the super  
desktop m boss give me at the lab.... (wow)

MAC OS X 10.5 came with ruby embedded in Developer tools.

Here is the gem env:

RubyGems Environment:
   - RUBYGEMS VERSION: 1.0.1 (1.0.1)
   - RUBY VERSION: 1.8.6 (2008-03-03 patchlevel 114) [universal- 
darwin9.0]
   - INSTALLATION DIRECTORY: /Library/Ruby/Gems/1.8
   - RUBYGEMS PREFIX: /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/lib/ruby
   - RUBY EXECUTABLE: /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/ruby
   - RUBYGEMS PLATFORMS:
     - ruby
     - universal-darwin-9
   - GEM PATHS:
      - /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ 
ruby/gems/1.8
      - /Library/Ruby/Gems/1.8
   - GEM CONFIGURATION:
      - :update_sources => true
      - :verbose => true
      - :benchmark => false
      - :backtrace => false
      - :bulk_threshold => 1000
   - REMOTE SOURCES:
      - http://gems.rubyforge.org



You may notice that installation directory are under /System/Library/ 
Frameworks/...    (you know: mac like to make developer life more  
complicated)

So now I retrieve the last bioruby from git with: git clone git:// 
github.com/bioruby/bioruby.git

I enter dir and I install in the canonical way:

ruby install.rb config
ruby install.rb setup


At this point the config.save file (is the file that stoe the urrent  
configuration sure?) contains:

bin-dir=$prefix/bin
prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
ruby-path=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
bin/ruby
make-prog=make
rb-dir=$site-ruby
without-ext=no
ruby-prog=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
bin/ruby
std-ruby=$prefix/lib/ruby/1.8
data-dir=$prefix/share


So all seems ok but when I try to install with:

sudo ruby install.rb install


install.rb: entering install phase...
---> bin
mkdir -p /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
install bioruby /System/Library/Frameworks/Ruby.framework/Versions/1.8/ 
usr/bin/
install br_biofetch.rb /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/
install br_bioflat.rb /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/
install br_biogetseq.rb /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/
install br_pmfetch.rb /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/
<--- bin
---> lib
mkdir -p /
install bio.rb /
---> lib/bio
mkdir -p /bio

[...] (continue)


ARGH!!!! after the bin install the install.rb install ALL the bio  
library in ROOT!

So to summarize:

- first bin are install correctly in /System/Library/.../usr/bin
- the ENTIRE library is installed in the wrong PATH (/)

Please notice that in another MAC with 10.5 really similar BUT with a  
manual installed version of ruby 1.8.7 in /url/local/bin the  
installation of bioruby is correct and all is installed in the correct  
path (in that case /usr/local/lib)

To conclude seems that there is a BUG in install.rb that is unable to  
install the bioruby library in /System/Library/Frameworks/ 
Ruby.framework/Version/1.8/usr/lib

If you don't have a MAC for testing, I can try to fix this, just give  
me some clues.

I have tried to specify the prefix with:

ruby install.rb setup --prefix=/System/Library/Frameworks/ 
Ruby.framework/Versions/1.8/usr

but in installation I have the same problem that is summarized by this  
2 lines of the install log!:

mkdir -p /
install bio.rb /


Again I can help you fix this, cause I have the right MAC to make  
tests, but I have no clues of where is the bug....


Best Regards


Davide Rambaldi, Bioinformatics PhD student.
-----------------------------------------------------
Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy
[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it 
 >
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi < 
%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi>  
(homepage)
[i] http://www.semm.it <http://www.semm.it/>             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)
-----------------------------------------------------



From adamnkraut at gmail.com  Mon Oct 13 14:07:07 2008
From: adamnkraut at gmail.com (Adam Kraut)
Date: Mon, 13 Oct 2008 10:07:07 -0400
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
In-Reply-To: <3D8E9D1A-CB03-46C5-B2F5-6FD46D96A4CD@ifom-ieo-campus.it>
References: <3D8E9D1A-CB03-46C5-B2F5-6FD46D96A4CD@ifom-ieo-campus.it>
Message-ID: <134ede0b0810130707j1315b8b2p40a4c423a353416e@mail.gmail.com>

Hi Davide,

Have you tried using the --prefix option for the 'install' command?  The
prefix only applies to the install task according to the help.  This appears
to be working OK for me on 10.5.5

/usr/bin/ruby install.rb install
--prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr

Note that I personally compile my own Ruby in /usr/local and don't recommend
using the Ruby supplied by Apple.  YMMV.

-Adam

On Mon, Oct 13, 2008 at 8:34 AM, Davide Rambaldi <
davide.rambaldi at ifom-ieo-campus.it> wrote:

> Hi all,
>
> the machine is an Intel Darwin 9.5.0 (MAC OSX 10.5.5), is the super desktop
> m boss give me at the lab.... (wow)
>
> MAC OS X 10.5 came with ruby embedded in Developer tools.
>
> Here is the gem env:
>
> RubyGems Environment:
>  - RUBYGEMS VERSION: 1.0.1 (1.0.1)
>  - RUBY VERSION: 1.8.6 (2008-03-03 patchlevel 114) [universal-darwin9.0]
>  - INSTALLATION DIRECTORY: /Library/Ruby/Gems/1.8
>  - RUBYGEMS PREFIX:
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby
>  - RUBY EXECUTABLE:
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
>  - RUBYGEMS PLATFORMS:
>    - ruby
>    - universal-darwin-9
>  - GEM PATHS:
>     -
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/gems/1.8
>     - /Library/Ruby/Gems/1.8
>  - GEM CONFIGURATION:
>     - :update_sources => true
>     - :verbose => true
>     - :benchmark => false
>     - :backtrace => false
>     - :bulk_threshold => 1000
>  - REMOTE SOURCES:
>     - http://gems.rubyforge.org
>
>
>
> You may notice that installation directory are under
> /System/Library/Frameworks/...    (you know: mac like to make developer life
> more complicated)
>
> So now I retrieve the last bioruby from git with: git clone git://
> github.com/bioruby/bioruby.git
>
> I enter dir and I install in the canonical way:
>
> ruby install.rb config
> ruby install.rb setup
>
>
> At this point the config.save file (is the file that stoe the urrent
> configuration sure?) contains:
>
> bin-dir=$prefix/bin
> prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
>
> ruby-path=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> make-prog=make
> rb-dir=$site-ruby
> without-ext=no
>
> ruby-prog=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> std-ruby=$prefix/lib/ruby/1.8
> data-dir=$prefix/share
>
>
> So all seems ok but when I try to install with:
>
> sudo ruby install.rb install
>
>
> install.rb: entering install phase...
> ---> bin
> mkdir -p /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install bioruby
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_biofetch.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_bioflat.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_biogetseq.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> install br_pmfetch.rb
> /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/
> <--- bin
> ---> lib
> mkdir -p /
> install bio.rb /
> ---> lib/bio
> mkdir -p /bio
>
> [...] (continue)
>
>
> ARGH!!!! after the bin install the install.rb install ALL the bio library
> in ROOT!
>
> So to summarize:
>
> - first bin are install correctly in /System/Library/.../usr/bin
> - the ENTIRE library is installed in the wrong PATH (/)
>
> Please notice that in another MAC with 10.5 really similar BUT with a
> manual installed version of ruby 1.8.7 in /url/local/bin the installation of
> bioruby is correct and all is installed in the correct path (in that case
> /usr/local/lib)
>
> To conclude seems that there is a BUG in install.rb that is unable to
> install the bioruby library in
> /System/Library/Frameworks/Ruby.framework/Version/1.8/usr/lib
>
> If you don't have a MAC for testing, I can try to fix this, just give me
> some clues.
>
> I have tried to specify the prefix with:
>
> ruby install.rb setup
> --prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
>
> but in installation I have the same problem that is summarized by this 2
> lines of the install log!:
>
> mkdir -p /
> install bio.rb /
>
>
> Again I can help you fix this, cause I have the right MAC to make tests,
> but I have no clues of where is the bug....
>
>
> Best Regards
>
>
> Davide Rambaldi, Bioinformatics PhD student.
> -----------------------------------------------------
> Bioinformatic Group IFOM-IEO Campus
> Via Adamello 16, Milano
> I-20139 Italy
> [t] +39 02574303 066
> [e] davide.rambaldi at ifom-ieo-campus.it <mailto:
> davide.rambaldi at ifom-ieo-campus.it>
> [i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi <%20
> http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi>
> (homepage)
> [i] http://www.semm.it <http://www.semm.it/>             (PhD school)
> [i] http://www.btbs.unimib.it/     (Master)
> -----------------------------------------------------
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby<https://lists.open-bio.org/mailman/listinfo/bioruby>
>


From davide.rambaldi at ifom-ieo-campus.it  Mon Oct 13 14:34:49 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Mon, 13 Oct 2008 16:34:49 +0200
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
In-Reply-To: <134ede0b0810130707j1315b8b2p40a4c423a353416e@mail.gmail.com>
References: <3D8E9D1A-CB03-46C5-B2F5-6FD46D96A4CD@ifom-ieo-campus.it>
	<134ede0b0810130707j1315b8b2p40a4c423a353416e@mail.gmail.com>
Message-ID: <8E8BC237-6E23-45F3-B516-14214653271D@ifom-ieo-campus.it>


On 13 Oct 2008, at 16:07, Adam Kraut wrote:

> Hi Davide,
>
> Have you tried using the --prefix option for the 'install' command?   
> The prefix only applies to the install task according to the help.   
> This appears to be working OK for me on 10.5.5
>
> /usr/bin/ruby install.rb install --prefix=/System/Library/Frameworks/ 
> Ruby.framework/Versions/1.8/usr


Yeah something similar (note the final lib) do the job:


sudo ruby install.rb install --prefix=/System/Library/Frameworks/ 
Ruby.framework/Versions/1.8/usr/lib/


BUT note the I have to specify also lib (or it will install in /System/ 
Library/Frameworks/Ruby.framework/Versions/1.8/usr/ an the library in  
unreachable)


NOW:


wst433:bioruby default$ irb
 >> require 'bio'
=> true


But (cause I have added the prefix /System/Library/Frameworks/ 
Ruby.framework/Versions/1.8/usr/lib/)

I have now the bin into:

/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/System/ 
Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/


terrible! :(

sigh

I hate MAC frameworks.....

>
>
> Note that I personally compile my own Ruby in /usr/local and don't  
> recommend using the Ruby supplied by Apple.  YMMV.
>

I am agree with you, and I have personally compiled my 1.8.7 ruby in / 
usr/local/bin

but may be is important to report the bug: automatic installation of  
bio.rb and bio directory in / (root) is painful for the general user

(imagine someone that see the error, want to remove /bio and for  
mistake type: sudo rm -rf / .... and the HD is gone! )



> -Adam
>
> On Mon, Oct 13, 2008 at 8:34 AM, Davide Rambaldi <davide.rambaldi at ifom-ieo-campus.it 
> > wrote:
> Hi all,
>
> the machine is an Intel Darwin 9.5.0 (MAC OSX 10.5.5), is the super  
> desktop m boss give me at the lab.... (wow)
>
> MAC OS X 10.5 came with ruby embedded in Developer tools.
>
> Here is the gem env:
>
> RubyGems Environment:
>  - RUBYGEMS VERSION: 1.0.1 (1.0.1)
>  - RUBY VERSION: 1.8.6 (2008-03-03 patchlevel 114) [universal- 
> darwin9.0]
>  - INSTALLATION DIRECTORY: /Library/Ruby/Gems/1.8
>  - RUBYGEMS PREFIX: /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/lib/ruby
>  - RUBY EXECUTABLE: /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/bin/ruby
>  - RUBYGEMS PLATFORMS:
>    - ruby
>    - universal-darwin-9
>  - GEM PATHS:
>     - /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ 
> ruby/gems/1.8
>     - /Library/Ruby/Gems/1.8
>  - GEM CONFIGURATION:
>     - :update_sources => true
>     - :verbose => true
>     - :benchmark => false
>     - :backtrace => false
>     - :bulk_threshold => 1000
>  - REMOTE SOURCES:
>     - http://gems.rubyforge.org
>
>
>
> You may notice that installation directory are under /System/Library/ 
> Frameworks/...    (you know: mac like to make developer life more  
> complicated)
>
> So now I retrieve the last bioruby from git with: git clone git:// 
> github.com/bioruby/bioruby.git
>
> I enter dir and I install in the canonical way:
>
> ruby install.rb config
> ruby install.rb setup
>
>
> At this point the config.save file (is the file that stoe the urrent  
> configuration sure?) contains:
>
> bin-dir=$prefix/bin
> prefix=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> ruby-path=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
> bin/ruby
> make-prog=make
> rb-dir=$site-ruby
> without-ext=no
> ruby-prog=/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
> bin/ruby
> std-ruby=$prefix/lib/ruby/1.8
> data-dir=$prefix/share
>
>
> So all seems ok but when I try to install with:
>
> sudo ruby install.rb install
>
>
> install.rb: entering install phase...
> ---> bin
> mkdir -p /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
> bin/
> install bioruby /System/Library/Frameworks/Ruby.framework/Versions/ 
> 1.8/usr/bin/
> install br_biofetch.rb /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/bin/
> install br_bioflat.rb /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/bin/
> install br_biogetseq.rb /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/bin/
> install br_pmfetch.rb /System/Library/Frameworks/Ruby.framework/ 
> Versions/1.8/usr/bin/
> <--- bin
> ---> lib
> mkdir -p /
> install bio.rb /
> ---> lib/bio
> mkdir -p /bio
>
> [...] (continue)
>
>
> ARGH!!!! after the bin install the install.rb install ALL the bio  
> library in ROOT!
>
> So to summarize:
>
> - first bin are install correctly in /System/Library/.../usr/bin
> - the ENTIRE library is installed in the wrong PATH (/)
>
> Please notice that in another MAC with 10.5 really similar BUT with  
> a manual installed version of ruby 1.8.7 in /url/local/bin the  
> installation of bioruby is correct and all is installed in the  
> correct path (in that case /usr/local/lib)
>
> To conclude seems that there is a BUG in install.rb that is unable  
> to install the bioruby library in /System/Library/Frameworks/ 
> Ruby.framework/Version/1.8/usr/lib
>
> If you don't have a MAC for testing, I can try to fix this, just  
> give me some clues.
>
> I have tried to specify the prefix with:
>
> ruby install.rb setup --prefix=/System/Library/Frameworks/ 
> Ruby.framework/Versions/1.8/usr
>
> but in installation I have the same problem that is summarized by  
> this 2 lines of the install log!:
>
> mkdir -p /
> install bio.rb /
>
>
> Again I can help you fix this, cause I have the right MAC to make  
> tests, but I have no clues of where is the bug....
>
>
> Best Regards
>
>
> Davide Rambaldi, Bioinformatics PhD student.
> -----------------------------------------------------
> Bioinformatic Group IFOM-IEO Campus
> Via Adamello 16, Milano
> I-20139 Italy
> [t] +39 02574303 066
> [e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it 
> >
> [i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi  
> <%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/ 
> DavideRambaldi> (homepage)
> [i] http://www.semm.it <http://www.semm.it/>             (PhD school)
> [i] http://www.btbs.unimib.it/     (Master)
> -----------------------------------------------------
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

Davide Rambaldi, Bioinformatics PhD student.
-----------------------------------------------------
Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy
[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it 
 >
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi < 
%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi>  
(homepage)
[i] http://www.semm.it <http://www.semm.it/>             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)
-----------------------------------------------------



From tomoakin at kenroku.kanazawa-u.ac.jp  Mon Oct 13 14:32:07 2008
From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA)
Date: Mon, 13 Oct 2008 23:32:07 +0900
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <9A8CA4BF-5DEE-402A-9A89-E266F139F0F9@ifom-ieo-campus.it>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<992DF6FE-14DF-45B9-B141-224FF473E82B@hgc.jp>
	<6B068F99-56FA-4E7E-AB60-887B83480F05@ifom-ieo-campus.it>
	<20080926133733.A99061CBC3F0@idnmail.gen-info.osaka-u.ac.jp>
	<9A8CA4BF-5DEE-402A-9A89-E266F139F0F9@ifom-ieo-campus.it>
Message-ID: <00B75F08-1B4E-45EE-A2E1-C873072A7F64@kenroku.kanazawa-u.ac.jp>

Hi,

> - For the database I have used the general db "sequences", assuming  
> that the method getent of entry.rb is only for sequences... is this  
> correct?


There are getseq and getent:
My feeling is that both the databases and libraries are growing
to handles datatypes other than sequences,
though the sequences have been the primary interest.
So, I would assume getent might be used in more general purpose than  
getting "sequences".

I suppose that having a database with possible db parameter string and
remote db and rettype combination is a extensible way to resolve the  
need for possible different
datatypes.
knowndbparams={"gb" => {"db" => sequences, "rettype" =>"gbwithparts"},
  "gp" => {"db" => sequences, "rettype" => "gp"},
...
}

and call like
fetch = Bio::NCBI::REST.efetch(entry_id, knwondbparams[db])

Note that with "rettype" =>"gb", large scaffolds that are composed of
several different contigs are obtained as a list of the individual
contig and without the actual sequence. This is good for the response  
time,
and the network load when the sequence part is not necessary,
but sometimes unexpected for the user.  Until it becomes to possible
to fetch the underlying sequence upon the access to the sequence of the
entry, "gbwithparts" seems the parameter to use as default.
-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan




From davide.rambaldi at ifom-ieo-campus.it  Mon Oct 13 16:05:06 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Mon, 13 Oct 2008 18:05:06 +0200
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <00B75F08-1B4E-45EE-A2E1-C873072A7F64@kenroku.kanazawa-u.ac.jp>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<992DF6FE-14DF-45B9-B141-224FF473E82B@hgc.jp>
	<6B068F99-56FA-4E7E-AB60-887B83480F05@ifom-ieo-campus.it>
	<20080926133733.A99061CBC3F0@idnmail.gen-info.osaka-u.ac.jp>
	<9A8CA4BF-5DEE-402A-9A89-E266F139F0F9@ifom-ieo-campus.it>
	<00B75F08-1B4E-45EE-A2E1-C873072A7F64@kenroku.kanazawa-u.ac.jp>
Message-ID: <E4D48C1F-1770-45DB-89CF-114B3224E8F0@ifom-ieo-campus.it>

>
>
> There are getseq and getent:
> My feeling is that both the databases and libraries are growing
> to handles datatypes other than sequences,
> though the sequences have been the primary interest.
> So, I would assume getent might be used in more general purpose than  
> getting "sequences".
>
> I suppose that having a database with possible db parameter string and
> remote db and rettype combination is a extensible way to resolve the  
> need for possible different
> datatypes.
> knowndbparams={"gb" => {"db" => sequences, "rettype" =>"gbwithparts"},
> "gp" => {"db" => sequences, "rettype" => "gp"},
> ...
> }
>
> and call like
> fetch = Bio::NCBI::REST.efetch(entry_id, knwondbparams[db])
>

I have modified to patch (see below), including a knowndbparams Hash.

Now work with:

bioruby> test = getobj("gb:AAF63163")
bioruby> test = getobj("gp:AF237819")


Actually the Hash handle genbank and genPept.

How I can add more datatypes?

I should take the definition in  NSIDs (lib/bio/io/dbget.rb) as key  
for knowdbparams Hash?

Here is (from NCBI website) the list of available db params for efetch:

1. EFETCH for literature
    db=[pubmed|pmc|journals|omim]

2. EFETCH for sequences
    	? gene
	? genome
	? nucleotide
	? nuccore
	? nucest
	? nucgss
	? protein
	? popset
	? snp
	? sequences - Composite name including nucleotide, protein, popset  
and genome.

3. EFETCH for taxonomy
    db=taxonomy


Best Regards

Davide

-------------------------------------------------------
PATCH HERE
----------------------------------------------------

Oni:bioruby tucano$ git diff
diff --git a/lib/bio.rb b/lib/bio.rb
index b2b6f4f..bddc221 100644
--- a/lib/bio.rb
+++ b/lib/bio.rb
@@ -170,6 +170,7 @@ module Bio

    class NCBI
      autoload :SOAP,       'bio/io/ncbisoap'
+    autoload :REST,       'bio/io/ncbirest'
    end


diff --git a/lib/bio/shell/plugin/entry.rb b/lib/bio/shell/plugin/ 
entry.rb
index 6d36fb5..2408a95 100644
--- a/lib/bio/shell/plugin/entry.rb
+++ b/lib/bio/shell/plugin/entry.rb
@@ -88,8 +88,19 @@ module Bio::Shell

        # KEGG API at http://www.genome.jp/kegg/soap/
        else
-        puts "Retrieving entry from KEGG API (#{arg})"
          entry = bget(arg)
+        if entry.length != 0 then
+          puts "Retrieving entry from KEGG API (#{arg})"
+        else
+          # NCBI efecth
+          knowndbparams = {
+            "gb" => {"db" => "sequences", "rettype" =>"gbwithparts"},
+            "gp" => {"db" => "sequences", "rettype" => "gp"}
+          }
+          puts "Retrieving entry from NCBI (#{arg})"
+          fetch = Bio::NCBI::REST.efetch(entry_id, knowndbparams[db])
+          entry = fetch.to_s
+        end
        end
      end





From andersbj at binf.ku.dk  Mon Oct 13 19:25:16 2008
From: andersbj at binf.ku.dk (Anders Jacobsen)
Date: Mon, 13 Oct 2008 21:25:16 +0200
Subject: [BioRuby] Biased Bio::Sequence randomize()
Message-ID: <000701c92d69$6dba9450$492fbcf0$@ku.dk>

Hi,

 

I believe that the current sequence randomization/shuffle method is severely
biased, infrequent bases are more likely to occur in the end of the sequence
than in the beginning:

 

class Array

  #returns a histogram represented as a hash

  def hist()

    h = Hash.new(0)

    self.each{|x| h[x] += 1}

    h

  end

end

 

>> (1..1000).to_a.map{|i|
Bio::Sequence::NA.new("ccccggac").randomize.index("a") + 1}.hist.sort

=> [[1, 36], [2, 51], [3, 62], [4, 97], [5, 127], [6, 189], [7, 219], [8,
219]]

 

I suggest implementing this method using the unbiased Fisher-Yates shuffle
(http://en.wikipedia.org/wiki/Fisher-Yates_shuffle)

 

class Array

  def shuffle()

    arr = self.dup

    arr.size.downto 2 do |j|

      r = Kernel::rand(j)

      arr[j-1], arr[r] = arr[r], arr[j-1]

    end

    arr

  end

end

 

(1..1000).to_a.map{|i|
Bio::Sequence::NA.new("ccccggac").split("").shuffle.index("a") +
1}.hist.sort

=> [[1, 121], [2, 127], [3, 135], [4, 119], [5, 145], [6, 104], [7, 126],
[8, 123]]

 

-Anders Jacobsen



From ktym at hgc.jp  Mon Oct 13 20:55:41 2008
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Tue, 14 Oct 2008 05:55:41 +0900
Subject: [BioRuby] Biased Bio::Sequence randomize()
In-Reply-To: <000701c92d69$6dba9450$492fbcf0$@ku.dk>
References: <000701c92d69$6dba9450$492fbcf0$@ku.dk>
Message-ID: <690F001A-C72C-4BF2-8056-E811D0431EAA@hgc.jp>

Dear Jacobsen,

> I believe that the current sequence randomization/shuffle method is severely
> biased, infrequent bases are more likely to occur in the end of the sequence
> than in the beginning:

You are right. 

I had fixed a while ago, but it seems that I forgot to commit to the repository, sorry.

Could you try the following replacement?

  def randomize(hash = nil)
    if hash
      tmp = ''
      hash.each {|k, v|
        tmp += k * v.to_i
      }
    else
      tmp = self
    end
    len = tmp.length - 1
    seq = ''
    ary = (0..len).to_a.sort_by{rand}
    ary.each do |idx|
      if block_given?
        yield tmp[idx]
      else
        seq << tmp[idx]
      end
    end
    return self.class.new(seq)
  end

I haven't yet prepared my git environment, so I hope someone (Goto-san?) can
take care of the following patch.

Regards,
Toshiaki Katayama


% cvs diff -u lib/bio/sequence/common.rb
===========================================
 dev.open-bio.org - Authorized Access Only
===========================================
Index: lib/bio/sequence/common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/common.rb,v
retrieving revision 1.6
diff -u -r1.6 common.rb
--- lib/bio/sequence/common.rb	27 Dec 2007 17:36:02 -0000	1.6
+++ lib/bio/sequence/common.rb	13 Oct 2008 20:50:27 -0000
@@ -241,28 +241,22 @@
   # * (optional) _hash_: Hash object
   # *Returns*:: new Bio::Sequence::NA/AA object
   def randomize(hash = nil)
-    length = self.length
     if hash
-      length = 0
-      count = hash.clone
-      count.each_value {|x| length += x}
+      tmp = ''
+      hash.each {|k, v|
+        tmp += k * v.to_i
+      }
     else
-      count = self.composition
+      tmp = self
     end
-
+    len = tmp.length - 1
     seq = ''
-    tmp = {}
-    length.times do 
-      count.each do |k, v|
-        tmp[k] = v * rand
-      end
-      max = tmp.max {|a, b| a[1] <=> b[1]}
-      count[max.first] -= 1
-
+    ary = (0..len).to_a.sort_by{rand}
+    ary.each do |idx|
       if block_given?
-        yield max.first
+        yield tmp[idx]
       else
-        seq += max.first
+        seq << tmp[idx]
       end
     end
     return self.class.new(seq)



On 2008/10/14, at 4:25, Anders Jacobsen wrote:

> Hi,
>
>
>
> I believe that the current sequence randomization/shuffle method is severely
> biased, infrequent bases are more likely to occur in the end of the sequence
> than in the beginning:
>
>
>
> class Array
>
>  #returns a histogram represented as a hash
>
>  def hist()
>
>    h = Hash.new(0)
>
>    self.each{|x| h[x] += 1}
>
>    h
>
>  end
>
> end
>
>
>
>>> (1..1000).to_a.map{|i|
> Bio::Sequence::NA.new("ccccggac").randomize.index("a") + 1}.hist.sort
>
> => [[1, 36], [2, 51], [3, 62], [4, 97], [5, 127], [6, 189], [7, 219], [8,
> 219]]
>
>
>
> I suggest implementing this method using the unbiased Fisher-Yates shuffle
> (http://en.wikipedia.org/wiki/Fisher-Yates_shuffle)
>
>
>
> class Array
>
>  def shuffle()
>
>    arr = self.dup
>
>    arr.size.downto 2 do |j|
>
>      r = Kernel::rand(j)
>
>      arr[j-1], arr[r] = arr[r], arr[j-1]
>
>    end
>
>    arr
>
>  end
>
> end
>
>
>
> (1..1000).to_a.map{|i|
> Bio::Sequence::NA.new("ccccggac").split("").shuffle.index("a") +
> 1}.hist.sort
>
> => [[1, 121], [2, 127], [3, 135], [4, 119], [5, 145], [6, 104], [7, 126],
> [8, 123]]
>
>
>
> -Anders Jacobsen
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby




From donttrustben at gmail.com  Tue Oct 14 04:51:40 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Tue, 14 Oct 2008 15:51:40 +1100
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <20081011075440.GA19106@thebird.nl>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
	<bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
	<20081011075440.GA19106@thebird.nl>
Message-ID: <bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>

Thanks for the encouragement. I've made an initial attempt at integrating
URL generation into BioRuby. I've made it available as my 'url' branch,
which is available at

http://github.com/wwood/bioruby/tree/url

Is this what you had in mind or am I misunderstanding you?

Thanks,
ben

2008/10/11 Pjotr Prins <pjotr2008 at thebird.nl>

> We could have a mixin module with methods that generate all different
> URLs in a central location. I think that is a good idea.
>
> Pj.
>
> On Sat, Oct 11, 2008 at 09:28:47AM +1100, Ben Woodcroft wrote:
> > Thanks for your response. I would have thought the fact that they change
> is
> > more reason to include it - not less.
> >
> > Is that database you speak of freely available? Just as part of the AceDB
> > download?
> >
> > Thanks,
> > ben
> >
> > 2008/10/10 Michael Han <mh6 at sanger.ac.uk>
> >
> > >
> > > On 10 Oct 2008, at 05:18, Ben Woodcroft wrote:
> > >
> > > Hi list,
> > >
> > > A common thing I find myself doing is to 'linkout' to other databases.
> For
> > > instance, I have a PDB id and I want to link to the corresponding
> record in
> > > pdb.org. Right now, I would have to go to the pdb site and try to
> reverse
> > > engineer it. In the past I've even had to email the webmasters for more
> > > information. It seems to me this is a duplication of effort, and so
> > > class(es) to collect this information for me might have a place in
> BioRuby.
> > >
> > > Does this sound reasonable to anyone? Is there any precendents out
> there?
> > > What might be a good way to structure the code?
> > >
> > > Thanks,
> > > ben
> > >
> > > --
> > > FYI: My email addresses at unimelb, uq and gmail all redirect to the
> same
> > > place.
> > > _______________________________________________
> > > BioRuby mailing list
> > > BioRuby at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioruby
> > >
> > >
> > > Hi Ben,
> > >
> > > what we did is save URL constructors in an database object in a sprintf
> > > style, which is in turn used by the xref objects linked to
> > > genes/proteins/etc.
> > > Anyway I am not sure if it is a good idea to put it in the bioruby
> library,
> > > as when you have a couple of dozens of different database, you can be
> sure
> > > that one URL will change every few days/weeks, so it is a hassle to
> keep all
> > > of them up-to-date.
> > > Michael
> > > ---------------------------------------
> > >   oo Wormbase Group, Sanger Institute
> > >   |  The Wellcome Trust Genome Campus,
> > >   |  Hinxton, Cambridge, CB10 1HH, UK.
> > >   |  Tel.: +44 (0)1223 49 6869
> > > --'
> > >
> > >
> > >
> > >
> > > -- The Wellcome Trust Sanger Institute is operated by Genome Research
> > > Limited, a charity registered in England with number 1021457 and a
> company
> > > registered in England with number 2742969, whose registered office is
> 215
> > > Euston Road, London, NW1 2BE.
> > >
> >
> >
> >
> > --
> > FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> > place.
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>



-- 
FYI: My email addresses at unimelb, uq and gmail all redirect to the same
place.


From adamnkraut at gmail.com  Tue Oct 14 15:04:23 2008
From: adamnkraut at gmail.com (Adam Kraut)
Date: Tue, 14 Oct 2008 11:04:23 -0400
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
	<bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
	<20081011075440.GA19106@thebird.nl>
	<bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>
Message-ID: <134ede0b0810140804m7fbd6005xf07ebbcef34a2529@mail.gmail.com>

I typically put these in Rails/Merb helpers.  I extracted a few from one of
my apps.  I'm still not sure if these belong in bioruby due to the huge
number of resources and urls.  I also think they're somewhat
project-specific.  You're welcome to include or modify these:

    def pdb_url_for(pdbId)
      "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#{pdbId}<http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#%7BpdbId%7D>
"
    end

    def pdbsum_url_for(pdbId)
      "
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#{pdbId}<http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#%7BpdbId%7D>
"
    end

    def cath_url_for(pdbId)
      "
http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#{pdbId}&type=PDB<http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#%7BpdbId%7D&type=PDB>
"
    end

    def scop_url_for(pdbId)
      "http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#{pdbId}<http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#%7BpdbId%7D>
"
    end

-Adam


From ktym at hgc.jp  Tue Oct 14 17:35:38 2008
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Wed, 15 Oct 2008 02:35:38 +0900
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <E4D48C1F-1770-45DB-89CF-114B3224E8F0@ifom-ieo-campus.it>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<992DF6FE-14DF-45B9-B141-224FF473E82B@hgc.jp>
	<6B068F99-56FA-4E7E-AB60-887B83480F05@ifom-ieo-campus.it>
	<20080926133733.A99061CBC3F0@idnmail.gen-info.osaka-u.ac.jp>
	<9A8CA4BF-5DEE-402A-9A89-E266F139F0F9@ifom-ieo-campus.it>
	<00B75F08-1B4E-45EE-A2E1-C873072A7F64@kenroku.kanazawa-u.ac.jp>
	<E4D48C1F-1770-45DB-89CF-114B3224E8F0@ifom-ieo-campus.it>
Message-ID: <020B141F-EC67-4FC5-A1EF-EF5C3F19638E@hgc.jp>

Hi,

I also forgot to commit my change to ncbirest.rb for TogoWS (http://togows.dbcls.jp/).
I'll attach my current version (Apr 18) and I hope some of you can take a look on it.

Regards,
Toshiaki Katayama

-------------- next part --------------




On 2008/10/14, at 1:05, Davide Rambaldi wrote:

>>
>>
>> There are getseq and getent:
>> My feeling is that both the databases and libraries are growing
>> to handles datatypes other than sequences,
>> though the sequences have been the primary interest.
>> So, I would assume getent might be used in more general purpose than getting "sequences".
>>
>> I suppose that having a database with possible db parameter string and
>> remote db and rettype combination is a extensible way to resolve the need for possible different
>> datatypes.
>> knowndbparams={"gb" => {"db" => sequences, "rettype" =>"gbwithparts"},
>> "gp" => {"db" => sequences, "rettype" => "gp"},
>> ...
>> }
>>
>> and call like
>> fetch = Bio::NCBI::REST.efetch(entry_id, knwondbparams[db])
>>
>
> I have modified to patch (see below), including a knowndbparams Hash.
>
> Now work with:
>
> bioruby> test = getobj("gb:AAF63163")
> bioruby> test = getobj("gp:AF237819")
>
>
> Actually the Hash handle genbank and genPept.
>
> How I can add more datatypes?
>
> I should take the definition in  NSIDs (lib/bio/io/dbget.rb) as key for knowdbparams Hash?
>
> Here is (from NCBI website) the list of available db params for efetch:
>
> 1. EFETCH for literature
>  db=[pubmed|pmc|journals|omim]
>
> 2. EFETCH for sequences
>  	? gene
> 	? genome
> 	? nucleotide
> 	? nuccore
> 	? nucest
> 	? nucgss
> 	? protein
> 	? popset
> 	? snp
> 	? sequences - Composite name including nucleotide, protein, popset and genome.
>
> 3. EFETCH for taxonomy
>  db=taxonomy
>
>
> Best Regards
>
> Davide
>
> -------------------------------------------------------
> PATCH HERE
> ----------------------------------------------------
>
> Oni:bioruby tucano$ git diff
> diff --git a/lib/bio.rb b/lib/bio.rb
> index b2b6f4f..bddc221 100644
> --- a/lib/bio.rb
> +++ b/lib/bio.rb
> @@ -170,6 +170,7 @@ module Bio
>
>  class NCBI
>    autoload :SOAP,       'bio/io/ncbisoap'
> +    autoload :REST,       'bio/io/ncbirest'
>  end
>
>
> diff --git a/lib/bio/shell/plugin/entry.rb b/lib/bio/shell/plugin/entry.rb
> index 6d36fb5..2408a95 100644
> --- a/lib/bio/shell/plugin/entry.rb
> +++ b/lib/bio/shell/plugin/entry.rb
> @@ -88,8 +88,19 @@ module Bio::Shell
>
>      # KEGG API at http://www.genome.jp/kegg/soap/
>      else
> -        puts "Retrieving entry from KEGG API (#{arg})"
>        entry = bget(arg)
> +        if entry.length != 0 then
> +          puts "Retrieving entry from KEGG API (#{arg})"
> +        else
> +          # NCBI efecth
> +          knowndbparams = {
> +            "gb" => {"db" => "sequences", "rettype" =>"gbwithparts"},
> +            "gp" => {"db" => "sequences", "rettype" => "gp"}
> +          }
> +          puts "Retrieving entry from NCBI (#{arg})"
> +          fetch = Bio::NCBI::REST.efetch(entry_id, knowndbparams[db])
> +          entry = fetch.to_s
> +        end
>      end
>    end
>
>
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From pjotr2008 at thebird.nl  Tue Oct 14 17:47:13 2008
From: pjotr2008 at thebird.nl (Pjotr Prins)
Date: Tue, 14 Oct 2008 19:47:13 +0200
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
	<bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
	<20081011075440.GA19106@thebird.nl>
	<bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>
Message-ID: <20081014174713.GA16130@thebird.nl>

Looks fine to me, I can add URLs for NCBI GEO access - Naohisa, what 
do you think?

Pj.

On Tue, Oct 14, 2008 at 03:51:40PM +1100, Ben Woodcroft wrote:
> Thanks for the encouragement. I've made an initial attempt at integrating
> URL generation into BioRuby. I've made it available as my 'url' branch,
> which is available at
> 
> http://github.com/wwood/bioruby/tree/url
> 
> Is this what you had in mind or am I misunderstanding you?
> 
> Thanks,
> ben
> 
> 2008/10/11 Pjotr Prins <pjotr2008 at thebird.nl>
> 
> > We could have a mixin module with methods that generate all different
> > URLs in a central location. I think that is a good idea.
> >
> > Pj.
> >
> > On Sat, Oct 11, 2008 at 09:28:47AM +1100, Ben Woodcroft wrote:
> > > Thanks for your response. I would have thought the fact that they change
> > is
> > > more reason to include it - not less.
> > >
> > > Is that database you speak of freely available? Just as part of the AceDB
> > > download?
> > >
> > > Thanks,
> > > ben
> > >
> > > 2008/10/10 Michael Han <mh6 at sanger.ac.uk>
> > >
> > > >
> > > > On 10 Oct 2008, at 05:18, Ben Woodcroft wrote:
> > > >
> > > > Hi list,
> > > >
> > > > A common thing I find myself doing is to 'linkout' to other databases.
> > For
> > > > instance, I have a PDB id and I want to link to the corresponding
> > record in
> > > > pdb.org. Right now, I would have to go to the pdb site and try to
> > reverse
> > > > engineer it. In the past I've even had to email the webmasters for more
> > > > information. It seems to me this is a duplication of effort, and so
> > > > class(es) to collect this information for me might have a place in
> > BioRuby.
> > > >
> > > > Does this sound reasonable to anyone? Is there any precendents out
> > there?
> > > > What might be a good way to structure the code?
> > > >
> > > > Thanks,
> > > > ben
> > > >
> > > > --
> > > > FYI: My email addresses at unimelb, uq and gmail all redirect to the
> > same
> > > > place.
> > > > _______________________________________________
> > > > BioRuby mailing list
> > > > BioRuby at lists.open-bio.org
> > > > http://lists.open-bio.org/mailman/listinfo/bioruby
> > > >
> > > >
> > > > Hi Ben,
> > > >
> > > > what we did is save URL constructors in an database object in a sprintf
> > > > style, which is in turn used by the xref objects linked to
> > > > genes/proteins/etc.
> > > > Anyway I am not sure if it is a good idea to put it in the bioruby
> > library,
> > > > as when you have a couple of dozens of different database, you can be
> > sure
> > > > that one URL will change every few days/weeks, so it is a hassle to
> > keep all
> > > > of them up-to-date.
> > > > Michael
> > > > ---------------------------------------
> > > >   oo Wormbase Group, Sanger Institute
> > > >   |  The Wellcome Trust Genome Campus,
> > > >   |  Hinxton, Cambridge, CB10 1HH, UK.
> > > >   |  Tel.: +44 (0)1223 49 6869
> > > > --'
> > > >
> > > >
> > > >
> > > >
> > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research
> > > > Limited, a charity registered in England with number 1021457 and a
> > company
> > > > registered in England with number 2742969, whose registered office is
> > 215
> > > > Euston Road, London, NW1 2BE.
> > > >
> > >
> > >
> > >
> > > --
> > > FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> > > place.
> > > _______________________________________________
> > > BioRuby mailing list
> > > BioRuby at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> 
> 
> 
> -- 
> FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> place.


From donttrustben at gmail.com  Wed Oct 15 01:07:59 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Wed, 15 Oct 2008 12:07:59 +1100
Subject: [BioRuby] URL Generation in Bioruby
In-Reply-To: <134ede0b0810140804m7fbd6005xf07ebbcef34a2529@mail.gmail.com>
References: <bb2b67d00810092118s3ea5a2e3lb28a1ef5d464a100@mail.gmail.com>
	<3E7FECB3-2111-4993-8532-C2E354205990@sanger.ac.uk>
	<bb2b67d00810101528y26deb060v7960549d00487e25@mail.gmail.com>
	<20081011075440.GA19106@thebird.nl>
	<bb2b67d00810132151p6cfe5c4ao71a35825e5a05597@mail.gmail.com>
	<134ede0b0810140804m7fbd6005xf07ebbcef34a2529@mail.gmail.com>
Message-ID: <bb2b67d00810141807t7547ff45kec9f62b8d802643d@mail.gmail.com>

Thanks Adam - I have included these into the module.

2008/10/15 Adam Kraut <adamnkraut at gmail.com>

> I typically put these in Rails/Merb helpers.  I extracted a few from one of
> my apps.  I'm still not sure if these belong in bioruby due to the huge
> number of resources and urls.  I also think they're somewhat
> project-specific.  You're welcome to include or modify these:
>
>     def pdb_url_for(pdbId)
>       "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#{pdbId}<http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#%7BpdbId%7D>
> "
>     end
>
>     def pdbsum_url_for(pdbId)
>       "
> http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#{pdbId}<http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#%7BpdbId%7D>
> "
>     end
>
>     def cath_url_for(pdbId)
>       "
> http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#{pdbId}&type=PDB<http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#%7BpdbId%7D&type=PDB>
> "
>     end
>
>     def scop_url_for(pdbId)
>       "http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#{pdbId}<http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#%7BpdbId%7D>
> "
>     end
>
> -Adam
>



-- 
FYI: My email addresses at unimelb, uq and gmail all redirect to the same
place.


From davide.rambaldi at ifom-ieo-campus.it  Wed Oct 15 10:26:44 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Wed, 15 Oct 2008 12:26:44 +0200
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
Message-ID: <AE11B0D0-8AB8-4B28-959B-7A5942B1FD45@ifom-ieo-campus.it>

About the installation of bioruby on a fresh MAC 10.5

I manage to install it in the correct path without install ruby in / 
usr/local/bin

Here is the story:

- I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/ 
   (setup-3.41.tar.gz)

- I just copy setup.rb in the bioruby directory (I still doesn't  
understand who generate install.rb for bioruby, is autogenerated I  
see, but with which ruby package?)

- I use the setup.rb file:

    * ruby setup.rb config
    * ruby setup.rb setup

At this point this is the config I have:

ruby setup.rb show

prefix               /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr
bindir               $prefix/bin
libdir               $prefix/lib
datadir              $prefix/share
mandir               /usr/share/man
sysconfdir           $prefix/etc
localstatedir        $prefix/var
libruby              /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/lib/ruby
librubyver           /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/lib/ruby/1.8
librubyverarch       /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0
siteruby             /Library/Ruby/Site
siterubyver          /Library/Ruby/Site/1.8
siterubyverarch      /Library/Ruby/Site/1.8/universal-darwin9.0
rbdir                $siterubyver
sodir                $siterubyverarch
rubypath             /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/ruby
rubyprog             /System/Library/Frameworks/Ruby.framework/ 
Versions/1.8/usr/bin/ruby
makeprog             make
shebang              ruby
without-ext          no



That compared with the config saved by install.rb is really different  
(the critical point id the siteruby path, that is in /Library/Ruby...):

ruby install.rb show
prefix     /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
std-ruby   $prefix/lib/ruby/1.8
site-ruby-common (not specified)
site-ruby  (not specified)
bin-dir    $prefix/bin
rb-dir     $site-ruby
so-dir     (not specified)
data-dir   $prefix/share
ruby-path  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
bin/ruby
ruby-prog  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/ 
bin/ruby
make-prog  make
without-ext no



Now I can run sudo ruby setup.rb install  (or ruby setup.rb install -- 
no-harm for just checking):

And the installation goes more or less well:

- all the lib files are installed into /Library/Ruby/Site/1.8

- the binary are installed in /System/Library/Frameworks/ 
Ruby.framework/Versions/1.8/usr/bin

So remains to do a post-install command to generate a link from / 
System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/bioruby  
to /usrbin/bioruby ....


END of the story.....


I will compile my personal ruby in /usr/local/bin amd renstall bioruby  
in any case: I have seen problems also with the rubygem update,  
etc....  :-(




Davide Rambaldi, Bioinformatics PhD student.
-----------------------------------------------------
Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy
[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it 
 >
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi < 
%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi>  
(homepage)
[i] http://www.semm.it <http://www.semm.it/>             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)
-----------------------------------------------------



From ktym at hgc.jp  Thu Oct 16 00:49:54 2008
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Thu, 16 Oct 2008 09:49:54 +0900
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
In-Reply-To: <AE11B0D0-8AB8-4B28-959B-7A5942B1FD45@ifom-ieo-campus.it>
References: <AE11B0D0-8AB8-4B28-959B-7A5942B1FD45@ifom-ieo-campus.it>
Message-ID: <5FC914E6-9F4A-4AEF-BF89-C0CDB603242D@hgc.jp>

Hi,

> - I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/  (setup-3.41.tar.gz)
>
> - I just copy setup.rb in the bioruby directory (I still doesn't understand who generate install.rb for bioruby, is autogenerated I see, but with which ruby package?)

install.rb in the BioRuby package is a old version of the setup (3.1.4)
>From your experiment, we should update it to the version 3.41. Thanks!

bioruby/README:
--------------------------------------------------
== LICENSE

BioRuby can be freely distributed under the same terms as Ruby.

Note that, install.rb included in the BioRuby package comes from
setup[http://raa.ruby-lang.org/project/setup/] developed by Minero Aoki,
and modified by Moses Hohman.
--------------------------------------------------

bioruby/ChangeLog:
--------------------------------------------------
2004-12-13  KATAYAMA Toshiaki <k at bioruby.org>

        * BioRuby 0.6.2 released.

        * test/all_tests.rb:

          Unit tests for some classes are newly incorporated by
          Moses Hohman.  You can try it by 'ruby install.rb test'

2003-06-25  KATAYAMA Toshiaki  <k at bioruby.org>

        * BioRuby version 0.5.0 released.

        * install.rb:

            Changed to use setup 3.1.4 to avoid installing CVS/ directory.
--------------------------------------------------

Regards,
Toshiaki Katayama


On 2008/10/15, at 19:26, Davide Rambaldi wrote:

> About the installation of bioruby on a fresh MAC 10.5
>
> I manage to install it in the correct path without install ruby in /usr/local/bin
>
> Here is the story:
>
> - I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/  (setup-3.41.tar.gz)
>
> - I just copy setup.rb in the bioruby directory (I still doesn't understand who generate install.rb for bioruby, is autogenerated I see, but with which ruby package?)
>
> - I use the setup.rb file:
>
>   * ruby setup.rb config
>   * ruby setup.rb setup
>
> At this point this is the config I have:
>
> ruby setup.rb show
>
> prefix               /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> bindir               $prefix/bin
> libdir               $prefix/lib
> datadir              $prefix/share
> mandir               /usr/share/man
> sysconfdir           $prefix/etc
> localstatedir        $prefix/var
> libruby              /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby
> librubyver           /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8
> librubyverarch       /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0
> siteruby             /Library/Ruby/Site
> siterubyver          /Library/Ruby/Site/1.8
> siterubyverarch      /Library/Ruby/Site/1.8/universal-darwin9.0
> rbdir                $siterubyver
> sodir                $siterubyverarch
> rubypath             /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> rubyprog             /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> makeprog             make
> shebang              ruby
> without-ext          no
>
>
>
> That compared with the config saved by install.rb is really different (the critical point id the siteruby path, that is in /Library/Ruby...):
>
> ruby install.rb show
> prefix     /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> std-ruby   $prefix/lib/ruby/1.8
> site-ruby-common (not specified)
> site-ruby  (not specified)
> bin-dir    $prefix/bin
> rb-dir     $site-ruby
> so-dir     (not specified)
> data-dir   $prefix/share
> ruby-path  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> ruby-prog  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> make-prog  make
> without-ext no
>
>
>
> Now I can run sudo ruby setup.rb install  (or ruby setup.rb install --no-harm for just checking):
>
> And the installation goes more or less well:
>
> - all the lib files are installed into /Library/Ruby/Site/1.8
>
> - the binary are installed in /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin
>
> So remains to do a post-install command to generate a link from /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/bioruby to /usrbin/bioruby ....
>
>
> END of the story.....
>
>
> I will compile my personal ruby in /usr/local/bin amd renstall bioruby in any case: I have seen problems also with the rubygem update, etc....  :-(
>
>
>
>
> Davide Rambaldi, Bioinformatics PhD student.
> -----------------------------------------------------
> Bioinformatic Group IFOM-IEO Campus
> Via Adamello 16, Milano
> I-20139 Italy
> [t] +39 02574303 066
> [e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it>
> [i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi <%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi> (homepage)
> [i] http://www.semm.it <http://www.semm.it/>             (PhD school)
> [i] http://www.btbs.unimib.it/     (Master)
> -----------------------------------------------------
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby





From ngoto at gen-info.osaka-u.ac.jp  Fri Oct 17 15:10:38 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 18 Oct 2008 00:10:38 +0900
Subject: [BioRuby] Biased Bio::Sequence randomize()
In-Reply-To: <690F001A-C72C-4BF2-8056-E811D0431EAA@hgc.jp>
References: <000701c92d69$6dba9450$492fbcf0$@ku.dk>
	<690F001A-C72C-4BF2-8056-E811D0431EAA@hgc.jp>
Message-ID: <20081017151038.67AD41CBC400@idnmail.gen-info.osaka-u.ac.jp>

Hi,

First, I implemented unit tests for Bio::Sequence::Common,
including chi-square test of equiprobability, and fixed the bug
by using Fisher-Yates shuffle, as suggested by Anders.

http://github.com/bioruby/bioruby/commit/02de70cbf036b41a50d770954f3b16ba2beca880
(Sorry for typo in the commit message)

On Tue, 14 Oct 2008 05:55:41 +0900
Toshiaki Katayama <ktym at hgc.jp> wrote:

> Dear Jacobsen,
> 
> > I believe that the current sequence randomization/shuffle method is severely
> > biased, infrequent bases are more likely to occur in the end of the sequence
> > than in the beginning:
> 
> You are right. 
> 
> I had fixed a while ago, but it seems that I forgot to commit to the repository, sorry.
> 
> Could you try the following replacement?

It works fine without blocks, but when giving a block,
the bahavior is different from the original one.
In addition, "(0..len).to_a.sort_by{rand}" is too expensive
when the sequence is long. So, I changed directly modifying
duplicated sequence, and fixed the bugs, based on your code.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org


From ngoto at gen-info.osaka-u.ac.jp  Sun Oct 19 05:15:10 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sun, 19 Oct 2008 14:15:10 +0900
Subject: [BioRuby] Installation from git repository on a MAC Intel 10.5.5
In-Reply-To: <5FC914E6-9F4A-4AEF-BF89-C0CDB603242D@hgc.jp>
References: <AE11B0D0-8AB8-4B28-959B-7A5942B1FD45@ifom-ieo-campus.it>
	<5FC914E6-9F4A-4AEF-BF89-C0CDB603242D@hgc.jp>
Message-ID: <20081019051510.CEB0E1CBC4B1@idnmail.gen-info.osaka-u.ac.jp>

Hi,

I get the setup.rb from Minero Aoki's svn repository
(see http://i.loveruby.net/en/projects/setup/ for details),
and replace install.rb with this newest setup.rb.
README.rdoc is also modified.

http://github.com/bioruby/bioruby/commit/9def7df5b81340c49534ff0bb932de62402a1c8d

Thanks,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 16 Oct 2008 09:49:54 +0900
Toshiaki Katayama <ktym at hgc.jp> wrote:

> Hi,
> 
> > - I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/  (setup-3.41.tar.gz)
> >
> > - I just copy setup.rb in the bioruby directory (I still doesn't understand who generate install.rb for bioruby, is autogenerated I see, but with which ruby package?)
> 
> install.rb in the BioRuby package is a old version of the setup (3.1.4)
> >From your experiment, we should update it to the version 3.41. Thanks!
> 
> bioruby/README:
> --------------------------------------------------
> == LICENSE
> 
> BioRuby can be freely distributed under the same terms as Ruby.
> 
> Note that, install.rb included in the BioRuby package comes from
> setup[http://raa.ruby-lang.org/project/setup/] developed by Minero Aoki,
> and modified by Moses Hohman.
> --------------------------------------------------
> 
> bioruby/ChangeLog:
> --------------------------------------------------
> 2004-12-13  KATAYAMA Toshiaki <k at bioruby.org>
> 
>         * BioRuby 0.6.2 released.
> 
>         * test/all_tests.rb:
> 
>           Unit tests for some classes are newly incorporated by
>           Moses Hohman.  You can try it by 'ruby install.rb test'
> 
> 2003-06-25  KATAYAMA Toshiaki  <k at bioruby.org>
> 
>         * BioRuby version 0.5.0 released.
> 
>         * install.rb:
> 
>             Changed to use setup 3.1.4 to avoid installing CVS/ directory.
> --------------------------------------------------
> 
> Regards,
> Toshiaki Katayama
> 
> 
> On 2008/10/15, at 19:26, Davide Rambaldi wrote:
> 
> > About the installation of bioruby on a fresh MAC 10.5
> >
> > I manage to install it in the correct path without install ruby in /usr/local/bin
> >
> > Here is the story:
> >
> > - I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/  (setup-3.41.tar.gz)
> >
> > - I just copy setup.rb in the bioruby directory (I still doesn't understand who generate install.rb for bioruby, is autogenerated I see, but with which ruby package?)
> >
> > - I use the setup.rb file:
> >
> >   * ruby setup.rb config
> >   * ruby setup.rb setup
> >
> > At this point this is the config I have:
> >
> > ruby setup.rb show
> >
> > prefix               /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> > bindir               $prefix/bin
> > libdir               $prefix/lib
> > datadir              $prefix/share
> > mandir               /usr/share/man
> > sysconfdir           $prefix/etc
> > localstatedir        $prefix/var
> > libruby              /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby
> > librubyver           /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8
> > librubyverarch       /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0
> > siteruby             /Library/Ruby/Site
> > siterubyver          /Library/Ruby/Site/1.8
> > siterubyverarch      /Library/Ruby/Site/1.8/universal-darwin9.0
> > rbdir                $siterubyver
> > sodir                $siterubyverarch
> > rubypath             /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > rubyprog             /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > makeprog             make
> > shebang              ruby
> > without-ext          no
> >
> >
> >
> > That compared with the config saved by install.rb is really different (the critical point id the siteruby path, that is in /Library/Ruby...):
> >
> > ruby install.rb show
> > prefix     /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> > std-ruby   $prefix/lib/ruby/1.8
> > site-ruby-common (not specified)
> > site-ruby  (not specified)
> > bin-dir    $prefix/bin
> > rb-dir     $site-ruby
> > so-dir     (not specified)
> > data-dir   $prefix/share
> > ruby-path  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > ruby-prog  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > make-prog  make
> > without-ext no
> >
> >
> >
> > Now I can run sudo ruby setup.rb install  (or ruby setup.rb install --no-harm for just checking):
> >
> > And the installation goes more or less well:
> >
> > - all the lib files are installed into /Library/Ruby/Site/1.8
> >
> > - the binary are installed in /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin
> >
> > So remains to do a post-install command to generate a link from /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/bioruby to /usrbin/bioruby ....
> >
> >
> > END of the story.....
> >
> >
> > I will compile my personal ruby in /usr/local/bin amd renstall bioruby in any case: I have seen problems also with the rubygem update, etc....  :-(
> >
> >
> >
> >
> > Davide Rambaldi, Bioinformatics PhD student.
> > -----------------------------------------------------
> > Bioinformatic Group IFOM-IEO Campus
> > Via Adamello 16, Milano
> > I-20139 Italy
> > [t] +39 02574303 066
> > [e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it>
> > [i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi <%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi> (homepage)
> > [i] http://www.semm.it <http://www.semm.it/>             (PhD school)
> > [i] http://www.btbs.unimib.it/     (Master)
> > -----------------------------------------------------
> >
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> 
> 
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From email2ants at gmail.com  Mon Oct 20 14:05:35 2008
From: email2ants at gmail.com (Anthony Underwood)
Date: Mon, 20 Oct 2008 15:05:35 +0100
Subject: [BioRuby] trace files (scf/abi) and ruby/bioruby
In-Reply-To: <20081003034209.939C81CBC434@idnmail.gen-info.osaka-u.ac.jp>
References: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>
	<4c7507a70810021104v7fd9c09dx57e317c2573e60a7@mail.gmail.com>
	<20081003034209.939C81CBC434@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <B866A193-D41A-49B4-8565-63F175099D80@gmail.com>

Work on the chromatogram reading classes in making good progress.  
Using a fork of the github bioruby repository I have been  
incorporating the classes into bioruby in the hope that it can be   
merged into the main bioruby repository.

However I have run into a problem with the to_biosequence method.
I have a Scf class that is a subclass of Chromatogram

Chromatogram has a method
     def to_biosequence
       Bio::Sequence.adapter(self, Bio::Sequence::Adapter::Chromatogram)
     end

I have added a line to autoload the  
Bio::Sequence::Adapter::Chromatogram module in the  
Bio::Sequence::Adapter Class.

The problem is that the to_biosequence method returns nil.

I have also found that this is the case when I test fasta and genbank  
sequences using  the existing Bio::FastaFormat and Bio::Genbank  
Classes when I use a fresh checkout of the main bioruby repository  
from github, so I don't think it's something I've done.

I see that the Bio::Sequence adapter method that to_biosequence calls  
is as follows

   def self.adapter(source_data, adapter_module)
     biosequence = self.new(nil)
     biosequence.instance_eval {
       remove_instance_variable(:@seq)
       @source_data = source_data
     }
     biosequence.extend(adapter_module)
     biosequence
   end

the last line does not return a biosequence even though if I puts  
biosequence.class just before the last line the output is Bio::Sequence.

Strangely if I insert the method call  biosequence.seq just before the  
last line of the adapter method everything is fine.

Does anybody know what's occurring here. Any help much appreciated.

Thanks

Anthony
On 3 Oct 2008, at 04:42, Naohisa GOTO wrote:

> Hi,
>
> For ABI traces, as far as I know, some person made previously,
> but all codes are lost now.
>
> http://open-bio.org/pipermail/bioruby/2005-September/000128.html
> but I cannot access to the URL described in the above archive.
>
> I don't remember why it wasn't included in bioruby, but,
> the thread of ML archive suggests that no one made any efforts
> to change the code adopting the development guideline.
>
> As Jan says, looking at bioperl, biopython, biojava, Staden, etc.
> and to write your own code seems good.
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
> On Thu, 2 Oct 2008 19:04:45 +0100
> "Jan Aerts" <jan.aerts at gmail.com> wrote:
>
>> If there's nothing there yet, you might have a look at the bioperl  
>> version
>> and take that as a guide.
>>
>> jan.
>>
>> 2008/10/2 Anthony Underwood <email2ants at gmail.com>
>>
>>> Hi all,
>>>
>>> Does anybody know if there is or someone is working on a ruby  
>>> module for
>>> reading abi/scf trace files. I was thinking of perhaps having a go  
>>> at this
>>> but thought I would check that there is no work in progress that I  
>>> should
>>> know about. I have done a few Google searches but come up with  
>>> nothing so
>>> thought I would ask on this list as well.
>>>
>>> Many thanks
>>>
>>> Anthony
>>> _______________________________________________
>>> BioRuby mailing list
>>> BioRuby at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>>
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From ngoto at gen-info.osaka-u.ac.jp  Mon Oct 20 15:21:18 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 21 Oct 2008 00:21:18 +0900
Subject: [BioRuby] trace files (scf/abi) and ruby/bioruby
In-Reply-To: <B866A193-D41A-49B4-8565-63F175099D80@gmail.com>
References: <D8086E9B-6399-4243-997C-580DC6635D49@gmail.com>
	<4c7507a70810021104v7fd9c09dx57e317c2573e60a7@mail.gmail.com>
	<20081003034209.939C81CBC434@idnmail.gen-info.osaka-u.ac.jp>
	<B866A193-D41A-49B4-8565-63F175099D80@gmail.com>
Message-ID: <20081020152119.4C6611CBC3E0@idnmail.gen-info.osaka-u.ac.jp>

Thank you.

Please tell us the URL of your git repository.

Which version of Ruby do you use?
% ruby -v 

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Mon, 20 Oct 2008 15:05:35 +0100
Anthony Underwood <email2ants at gmail.com> wrote:

> Work on the chromatogram reading classes in making good progress.  
> Using a fork of the github bioruby repository I have been  
> incorporating the classes into bioruby in the hope that it can be   
> merged into the main bioruby repository.
>
> However I have run into a problem with the to_biosequence method.
> I have a Scf class that is a subclass of Chromatogram
> 
> Chromatogram has a method
>      def to_biosequence
>        Bio::Sequence.adapter(self, Bio::Sequence::Adapter::Chromatogram)
>      end
> 
> I have added a line to autoload the  
> Bio::Sequence::Adapter::Chromatogram module in the  
> Bio::Sequence::Adapter Class.
> 
> The problem is that the to_biosequence method returns nil.
> 
> I have also found that this is the case when I test fasta and genbank  
> sequences using  the existing Bio::FastaFormat and Bio::Genbank  
> Classes when I use a fresh checkout of the main bioruby repository  
> from github, so I don't think it's something I've done.
> 
> I see that the Bio::Sequence adapter method that to_biosequence calls  
> is as follows
> 
>    def self.adapter(source_data, adapter_module)
>      biosequence = self.new(nil)
>      biosequence.instance_eval {
>        remove_instance_variable(:@seq)
>        @source_data = source_data
>      }
>      biosequence.extend(adapter_module)
>      biosequence
>    end
> 
> the last line does not return a biosequence even though if I puts  
> biosequence.class just before the last line the output is Bio::Sequence.
> 
> Strangely if I insert the method call  biosequence.seq just before the  
> last line of the adapter method everything is fine.
> 
> Does anybody know what's occurring here. Any help much appreciated.
> 
> Thanks
> 
> Anthony
> On 3 Oct 2008, at 04:42, Naohisa GOTO wrote:
> 
> > Hi,
> >
> > For ABI traces, as far as I know, some person made previously,
> > but all codes are lost now.
> >
> > http://open-bio.org/pipermail/bioruby/2005-September/000128.html
> > but I cannot access to the URL described in the above archive.
> >
> > I don't remember why it wasn't included in bioruby, but,
> > the thread of ML archive suggests that no one made any efforts
> > to change the code adopting the development guideline.
> >
> > As Jan says, looking at bioperl, biopython, biojava, Staden, etc.
> > and to write your own code seems good.
> >
> > Naohisa Goto
> > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> >
> > On Thu, 2 Oct 2008 19:04:45 +0100
> > "Jan Aerts" <jan.aerts at gmail.com> wrote:
> >
> >> If there's nothing there yet, you might have a look at the bioperl  
> >> version
> >> and take that as a guide.
> >>
> >> jan.
> >>
> >> 2008/10/2 Anthony Underwood <email2ants at gmail.com>
> >>
> >>> Hi all,
> >>>
> >>> Does anybody know if there is or someone is working on a ruby  
> >>> module for
> >>> reading abi/scf trace files. I was thinking of perhaps having a go  
> >>> at this
> >>> but thought I would check that there is no work in progress that I  
> >>> should
> >>> know about. I have done a few Google searches but come up with  
> >>> nothing so
> >>> thought I would ask on this list as well.
> >>>
> >>> Many thanks
> >>>
> >>> Anthony
> >>> _______________________________________________
> >>> BioRuby mailing list
> >>> BioRuby at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioruby
> >>>
> >> _______________________________________________
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> 



From georgkam at gmail.com  Thu Oct 23 06:15:42 2008
From: georgkam at gmail.com (George Githinji)
Date: Thu, 23 Oct 2008 09:15:42 +0300
Subject: [BioRuby] can the real official bioruby site standup?
Message-ID: <55915f820810222315m1632fe8bo32849e99c5f2269a@mail.gmail.com>

Hi,
Just wondering, which is the official bioruby site?
this one
http://bioruby.open-bio.org/

or
http://www.bioruby.org/

The first one seems to be well designed and very nice,  Is it possible
for bioruby.org domain to automatically redirect to
http://bioruby.open-bio.org/

Thanks
--
---------------
Sincerely
George

Skype: george_g2
Website: http://biorelated.wordpress.com/


From mauricio at open-bio.org  Thu Oct 23 15:08:44 2008
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Thu, 23 Oct 2008 10:08:44 -0500
Subject: [BioRuby] can the real official bioruby site standup?
In-Reply-To: <55915f820810222315m1632fe8bo32849e99c5f2269a@mail.gmail.com>
References: <55915f820810222315m1632fe8bo32849e99c5f2269a@mail.gmail.com>
Message-ID: <4900937C.4040401@open-bio.org>

Hi George,

There's a pending request at the OBF Helpdesk to have this redirect set 
up, however, Toshiaki has DNS control of the bioruby.org domain and he 
would need to point it to the IP address for the bioruby.open-bio.org site.

Regards,
Mauricio.


George Githinji wrote:
> Hi,
> Just wondering, which is the official bioruby site?
> this one
> http://bioruby.open-bio.org/
> 
> or
> http://www.bioruby.org/
> 
> The first one seems to be well designed and very nice,  Is it possible
> for bioruby.org domain to automatically redirect to
> http://bioruby.open-bio.org/
> 
> Thanks
> --
> ---------------
> Sincerely
> George
> 
> Skype: george_g2
> Website: http://biorelated.wordpress.com/
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
> 


From ixpata at gmail.com  Thu Oct 23 15:15:50 2008
From: ixpata at gmail.com (Steve Mitchell)
Date: Thu, 23 Oct 2008 11:15:50 -0400
Subject: [BioRuby]  bioruby tutorials?
Message-ID: <74b8d37e0810230815j294c05f7sa3b1e669a2008a61@mail.gmail.com>

>
> Anybody know of any good bioruby tutorials? I started going through the
> wiki bioruby tutorial, but I'm pretty new and I think I need something more
> basic or maybe something with exercises that would require me to put some of
> this stuff into practice.
>

Thanks.


From jan.aerts at gmail.com  Thu Oct 23 15:25:29 2008
From: jan.aerts at gmail.com (Jan Aerts)
Date: Thu, 23 Oct 2008 16:25:29 +0100
Subject: [BioRuby] bioruby tutorials?
In-Reply-To: <74b8d37e0810230815j294c05f7sa3b1e669a2008a61@mail.gmail.com>
References: <74b8d37e0810230815j294c05f7sa3b1e669a2008a61@mail.gmail.com>
Message-ID: <4c7507a70810230825m4f047146n2f9adb00df2122e4@mail.gmail.com>

I really like the tutorials that are provided on the bio*perl* website (
http://www.bioperl.org/wiki/HOWTOs). The bioperl documentation explains how
each class works (exactly like the bioruby rdoc), but the howtos take a
problem-oriented approach. They explain how to tackle a certain problem
which might include cross-class interactions.

At the moment we don't have any of these tutorials on the website yet (there
obviously _is_ the general tutorial, but some more specific howtos would be
good) and I don't know if anyone is actually working on one. If anyone has
an idea on how to get people writing these tutorials: let us know!

jan.



2008/10/23 Steve Mitchell <ixpata at gmail.com>

> >
> > Anybody know of any good bioruby tutorials? I started going through the
> > wiki bioruby tutorial, but I'm pretty new and I think I need something
> more
> > basic or maybe something with exercises that would require me to put some
> of
> > this stuff into practice.
> >
>
> Thanks.
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>