From mail at michaelbarton.me.uk  Thu Aug  7 11:20:23 2008
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Thu, 7 Aug 2008 16:20:23 +0100
Subject: [BioRuby] Problem with autoload in lib/bio.rb
Message-ID: <c27b73c0808070820n45a90cdaia917ff974927ec46@mail.gmail.com>

Hello,

I'm currently having some problems trying to use BioRuby from the source.
Specifically I'm having problems try to access some of the applications
defined using autoload in irb.

For example

> require 'lib/bio'
> Bio::Iprscan
LoadError: no such file to load -- bio/appl/iprscan/report
    from (irb):4

Could anyone provide a suggestion as to what I'm doing wrong? I'm some what
stuck at this point.

Thanks

Mike

From pjotr2008 at thebird.nl  Thu Aug  7 11:30:44 2008
From: pjotr2008 at thebird.nl (Pjotr Prins)
Date: Thu, 7 Aug 2008 17:30:44 +0200
Subject: [BioRuby] Problem with autoload in lib/bio.rb
In-Reply-To: <c27b73c0808070820n45a90cdaia917ff974927ec46@mail.gmail.com>
References: <c27b73c0808070820n45a90cdaia917ff974927ec46@mail.gmail.com>
Message-ID: <20080807153044.GA28970@thebird.nl>

Are you giving an include path (-I with ruby, or RUBYLIB environment
variable)? In irb you may be able to do:

$: << 'pathtobioruby/bioruby/lib'
require 'bio'


On Thu, Aug 07, 2008 at 04:20:23PM +0100, Michael Barton wrote:
> Hello,
> 
> I'm currently having some problems trying to use BioRuby from the source.
> Specifically I'm having problems try to access some of the applications
> defined using autoload in irb.
> 
> For example
> 
> > require 'lib/bio'
> > Bio::Iprscan
> LoadError: no such file to load -- bio/appl/iprscan/report
>     from (irb):4
> 
> Could anyone provide a suggestion as to what I'm doing wrong? I'm some what
> stuck at this point.
> 
> Thanks
> 
> Mike
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

From mail at michaelbarton.me.uk  Fri Aug  8 10:02:09 2008
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Fri, 8 Aug 2008 15:02:09 +0100
Subject: [BioRuby] Problem with autoload in lib/bio.rb
In-Reply-To: <20080807153044.GA28970@thebird.nl>
References: <c27b73c0808070820n45a90cdaia917ff974927ec46@mail.gmail.com>
	<20080807153044.GA28970@thebird.nl>
Message-ID: <c27b73c0808080702t1097a842lcc64249ab2690c28@mail.gmail.com>

Thanks Pjotr, that works. I'm having some trouble getting something similar
to work with active_resource though, where I have to explicitly require each
app.

For example

require 'bio'
require 'bio/appl/iprscan'

I wonder if you have ever come across something like this before?

Thanks

Mike


On Thu, Aug 7, 2008 at 4:30 PM, Pjotr Prins <pjotr2008 at thebird.nl> wrote:

> Are you giving an include path (-I with ruby, or RUBYLIB environment
> variable)? In irb you may be able to do:
>
> $: << 'pathtobioruby/bioruby/lib'
> require 'bio'
>
>
> On Thu, Aug 07, 2008 at 04:20:23PM +0100, Michael Barton wrote:
> > Hello,
> >
> > I'm currently having some problems trying to use BioRuby from the source.
> > Specifically I'm having problems try to access some of the applications
> > defined using autoload in irb.
> >
> > For example
> >
> > > require 'lib/bio'
> > > Bio::Iprscan
> > LoadError: no such file to load -- bio/appl/iprscan/report
> >     from (irb):4
> >
> > Could anyone provide a suggestion as to what I'm doing wrong? I'm some
> what
> > stuck at this point.
> >
> > Thanks
> >
> > Mike
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>

From gtraub at flmnh.ufl.edu  Tue Aug 12 14:09:56 2008
From: gtraub at flmnh.ufl.edu (Greg Traub)
Date: Tue, 12 Aug 2008 14:09:56 -0400
Subject: [BioRuby] Help with Bio::Blast
Message-ID: <48A1D1F4.5040704@flmnh.ufl.edu>

Hello,

I'm new to BioRuby but not new to Ruby. I've been trying to write code 
to submit a fasta formated sequence for BLAST search, however I never 
get back anything thats usable. After reading the documentation, I 
should be receiving xml formated responses to my search, but I dont 
receive anything. I altered the code in Bio::Blast class to print out 
whatever raw data was being sent back from my request and to my 
surprise, I keep receiving standard formated HTML page that tells me my 
request is either requesting the wrong program or the wrong database . 
I've been trying to use 'blastn' with 'nr' or 'nr-nt' ...documentation 
seems differ as to what the name of the databases are, so I've tried all 
of them with no luck. Now what really gets me is that i should be 
getting back XML. I would even an expect the error message to be in XML 
but instead its in a  HTML page  with javascript included.  This makes 
me think that the request is going to URL not intended for XML 
responses. Can anybody help me?  I've pasted some example code that I've 
tried below.

Thanks,
Greg

#files is array of file locations
#res is response
#im just trying to get back any info i can from the request
#in the example code below

blast = Bio::Blast.remote('blastn','nr')
files.each do |file|
     Bio::FastaFormat.open(file).each_entry do |c|
        reports = blast.query(c.seq)
        reports.each { |report| res << report.query_seq }
     end
end

-- 
Database Programmer
Florida Museum of Natural History
University of Florida
gtraub at flmnh.ufl.edu
(352) 392-1721 ext. 514
----------------------------------

Experience is what you get when
you didn't get what you want.
-National Vacuum sign


From donttrustben at gmail.com  Tue Aug 12 23:59:03 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Wed, 13 Aug 2008 13:59:03 +1000
Subject: [BioRuby] Help with Bio::Blast
In-Reply-To: <48A1D1F4.5040704@flmnh.ufl.edu>
References: <48A1D1F4.5040704@flmnh.ufl.edu>
Message-ID: <bb2b67d00808122059s77b7b142od69ff3085e2181d4@mail.gmail.com>

I don't personally use the bioruby blast interface because I'm more
used to the plain old blast command line interface, but I can suggest
a workaround. What if you just put '-m 7' (ie blast output) in the
options?

The only other problem is that the new version of blast XML isn't well
supported by bioruby. Read the bug report for more information:
http://rubyforge.org/tracker/index.php?func=detail&aid=20272&group_id=769&atid=3037

Thanks,
ben

2008/8/13 Greg Traub <gtraub at flmnh.ufl.edu>:
> Hello,
>
> I'm new to BioRuby but not new to Ruby. I've been trying to write code to
> submit a fasta formated sequence for BLAST search, however I never get back
> anything thats usable. After reading the documentation, I should be
> receiving xml formated responses to my search, but I dont receive anything.
> I altered the code in Bio::Blast class to print out whatever raw data was
> being sent back from my request and to my surprise, I keep receiving
> standard formated HTML page that tells me my request is either requesting
> the wrong program or the wrong database . I've been trying to use 'blastn'
> with 'nr' or 'nr-nt' ...documentation seems differ as to what the name of
> the databases are, so I've tried all of them with no luck. Now what really
> gets me is that i should be getting back XML. I would even an expect the
> error message to be in XML but instead its in a  HTML page  with javascript
> included.  This makes me think that the request is going to URL not intended
> for XML responses. Can anybody help me?  I've pasted some example code that
> I've tried below.
>
> Thanks,
> Greg
>
> #files is array of file locations
> #res is response
> #im just trying to get back any info i can from the request
> #in the example code below
>
> blast = Bio::Blast.remote('blastn','nr')
> files.each do |file|
>    Bio::FastaFormat.open(file).each_entry do |c|
>       reports = blast.query(c.seq)
>       reports.each { |report| res << report.query_seq }
>    end
> end
>
> --
> Database Programmer
> Florida Museum of Natural History
> University of Florida
> gtraub at flmnh.ufl.edu
> (352) 392-1721 ext. 514
> ----------------------------------
>
> Experience is what you get when
> you didn't get what you want.
> -National Vacuum sign
>
> _______________________________________________
> 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 ngoto at gen-info.osaka-u.ac.jp  Tue Aug 12 23:53:17 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Wed, 13 Aug 2008 12:53:17 +0900
Subject: [BioRuby] Help with Bio::Blast
In-Reply-To: <48A1D1F4.5040704@flmnh.ufl.edu>
References: <48A1D1F4.5040704@flmnh.ufl.edu>
Message-ID: <20080813035317.A46F11CBC3C3@idnmail.gen-info.osaka-u.ac.jp>

Hello,

Related topic: 
http://lists.open-bio.org/pipermail/bioruby/2008-July/000664.html

I modified your code below.
However, because of the change of the behavior of remote site
(http://blast.genome.jp/), it may not work with long query sequences.

  res = []
  blast = Bio::Blast.remote('blastn', 'nr-nt', '-e 0.1')
  files.each do |file|
     Bio::FlatFile.foreach(Bio::FastaFormat, file) do |c|
        reports = blast.query(c.naseq.to_fasta(c.definition, 70))
        reports.each { |report| res << report.query_seq }
     end
  end

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

On Tue, 12 Aug 2008 14:09:56 -0400
Greg Traub <gtraub at flmnh.ufl.edu> wrote:

> Hello,
> 
> I'm new to BioRuby but not new to Ruby. I've been trying to write code 
> to submit a fasta formated sequence for BLAST search, however I never 
> get back anything thats usable. After reading the documentation, I 
> should be receiving xml formated responses to my search, but I dont 
> receive anything. I altered the code in Bio::Blast class to print out 
> whatever raw data was being sent back from my request and to my 
> surprise, I keep receiving standard formated HTML page that tells me my 
> request is either requesting the wrong program or the wrong database . 
> I've been trying to use 'blastn' with 'nr' or 'nr-nt' ...documentation 
> seems differ as to what the name of the databases are, so I've tried all 
> of them with no luck. Now what really gets me is that i should be 
> getting back XML. I would even an expect the error message to be in XML 
> but instead its in a  HTML page  with javascript included.  This makes 
> me think that the request is going to URL not intended for XML 
> responses. Can anybody help me?  I've pasted some example code that I've 
> tried below.
> 
> Thanks,
> Greg
> 
> #files is array of file locations
> #res is response
> #im just trying to get back any info i can from the request
> #in the example code below
> 
> blast = Bio::Blast.remote('blastn','nr')
> files.each do |file|
>      Bio::FastaFormat.open(file).each_entry do |c|
>         reports = blast.query(c.seq)
>         reports.each { |report| res << report.query_seq }
>      end
> end
> 
> -- 
> Database Programmer
> Florida Museum of Natural History
> University of Florida
> gtraub at flmnh.ufl.edu
> (352) 392-1721 ext. 514
> ----------------------------------
> 
> Experience is what you get when
> you didn't get what you want.
> -National Vacuum sign
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From mail at michaelbarton.me.uk  Wed Aug 13 11:34:20 2008
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Wed, 13 Aug 2008 16:34:20 +0100
Subject: [BioRuby] CodeML wrapper for BioRuby
Message-ID: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>

Hi,

CodeML is a common tool for estimating evolutionary rate of protein encoding
sequences, and is part of the PAML package. I've created a codeml wrapper
and two parsers. Unit tests are also included. The code is in a Github fork
in BioRuby. The fork is located here

http://github.com/michaelbarton/bioruby/tree/master

I like to suggested that it for inclusion in the main BioRuby branch.

Thanks

Mike

From ngoto at gen-info.osaka-u.ac.jp  Fri Aug 15 07:15:09 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Fri, 15 Aug 2008 20:15:09 +0900
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
Message-ID: <20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>

Hi, 

It seems good. It will be included in BioRuby.

In my machine, a test was failed.
Can you fix the problem?
------------------------------------------------------------
$ ruby test/unit/bio/appl/test_codeml.rb
Loaded suite test/unit/bio/appl/test_codeml
Started
..F....
Finished in 0.032717 seconds.

  1) Failure:
test_correct_options_should_be_loaded(Bio::TestConfigFileUsage) [test/unit/bio/appl/test_codeml.rb:87]:
<"/xxxxx/ngoto/work/test/data/codeml/abglobin.aa"> expected but was
<"/xxxxx/ngoto/work/bioruby/git/michaelbarton/bioruby/test/data/codeml/abglobin.aa">.

7 tests, 9 assertions, 1 failures, 0 errors
------------------------------------------------------------
(some part of file path is masked with "xxxxx")


On Wed, 13 Aug 2008 16:34:20 +0100
"Michael Barton" <mail at michaelbarton.me.uk> wrote:

> Hi,
> 
> CodeML is a common tool for estimating evolutionary rate of protein encoding
> sequences, and is part of the PAML package. I've created a codeml wrapper
> and two parsers. Unit tests are also included. The code is in a Github fork
> in BioRuby. The fork is located here
> 
> http://github.com/michaelbarton/bioruby/tree/master
> 
> I like to suggested that it for inclusion in the main BioRuby branch.
> 
> Thanks
> 
> Mike
> _______________________________________________
> 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  Sat Aug 16 04:45:21 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 16 Aug 2008 17:45:21 +0900
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>

Hi Mike,

The CodeML wrappers is now included in bioruby git.
http://github.com/bioruby/bioruby/tree/master

As PAML has some executables other than codeml,
(baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
I plan to move Bio::CodeML to Bio::PAML::CodeML, and
files are moved from bio/appl/codeml to bio/appl/paml/codeml.

Is it OK? (or, is codeml the only valuable component to write
wrapper/parser for bioruby?)

Do you (or someone) plan to write other PAML's wrappers/parsers?

Thanks,

Naohisa Goto
ngoto at bioruby.org / ng at bioruby.org


On Fri, 15 Aug 2008 20:15:09 +0900
Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:

> Hi, 
> 
> It seems good. It will be included in BioRuby.
> 
> In my machine, a test was failed.
> Can you fix the problem?
(snip)
>
> On Wed, 13 Aug 2008 16:34:20 +0100
> "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> 
> > Hi,
> > 
> > CodeML is a common tool for estimating evolutionary rate of protein encoding
> > sequences, and is part of the PAML package. I've created a codeml wrapper
> > and two parsers. Unit tests are also included. The code is in a Github fork
> > in BioRuby. The fork is located here
> > 
> > http://github.com/michaelbarton/bioruby/tree/master
> > 
> > I like to suggested that it for inclusion in the main BioRuby branch.
> > 
> > Thanks
> > 
> > Mike
> > _______________________________________________
> > 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


-- 
?? ??  ngoto at gen-info.osaka-u.ac.jp
??????????? ?????????? ?????????(???)
Phone: 06-6879-8365 / FAX: 06-6879-2047

From pjotr2008 at thebird.nl  Sat Aug 16 12:22:18 2008
From: pjotr2008 at thebird.nl (Pjotr Prins)
Date: Sat, 16 Aug 2008 18:22:18 +0200
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
	<20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <20080816162218.GA4512@thebird.nl>

codeml is, by far, the most valuable tool.

Pj.

On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> Hi Mike,
> 
> The CodeML wrappers is now included in bioruby git.
> http://github.com/bioruby/bioruby/tree/master
> 
> As PAML has some executables other than codeml,
> (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> 
> Is it OK? (or, is codeml the only valuable component to write
> wrapper/parser for bioruby?)
> 
> Do you (or someone) plan to write other PAML's wrappers/parsers?
> 
> Thanks,
> 
> Naohisa Goto
> ngoto at bioruby.org / ng at bioruby.org
> 
> 
> On Fri, 15 Aug 2008 20:15:09 +0900
> Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> 
> > Hi, 
> > 
> > It seems good. It will be included in BioRuby.
> > 
> > In my machine, a test was failed.
> > Can you fix the problem?
> (snip)
> >
> > On Wed, 13 Aug 2008 16:34:20 +0100
> > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > 
> > > Hi,
> > > 
> > > CodeML is a common tool for estimating evolutionary rate of protein encoding
> > > sequences, and is part of the PAML package. I've created a codeml wrapper
> > > and two parsers. Unit tests are also included. The code is in a Github fork
> > > in BioRuby. The fork is located here
> > > 
> > > http://github.com/michaelbarton/bioruby/tree/master
> > > 
> > > I like to suggested that it for inclusion in the main BioRuby branch.
> > > 
> > > Thanks
> > > 
> > > Mike
> > > _______________________________________________
> > > 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
> 
> 
> -- 
> ?$B8eF# ?$BD>5W  ngoto at gen-info.osaka-u.ac.jp
> ?$BBg:eBg3XHy at 8J*IB8&5f=j ?$B0dEA>pJs<B83%;%s%?!< ?$B%2%N%`>pJs2r at OJ,Ln(?$B0B1J8&)
> Phone: 06-6879-8365 / FAX: 06-6879-2047
> _______________________________________________
> 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 Aug 18 02:18:38 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 18 Aug 2008 15:18:38 +0900
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <20080816162218.GA4512@thebird.nl>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
	<20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
	<20080816162218.GA4512@thebird.nl>
Message-ID: <20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>

Thank you.

I think PAML programs other than codeml are also valuale
to write wrappers, especially for baseml and yn00.

In BioPerl, there are four PAML program wrappers.
(baseml, codeml, evolver, yn00)
http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML

So, I decide to move the codeml classes under Bio::PAML.  

I renamed Bio::CodeML to Bio::PAML::Codeml. Files are moved
to bio/appl/paml/ and test/unit/bio/appl/paml/.

The reason why I changed CodeML to Codeml is that
it seems that authors of PAML do not use the word "codeML"
(the last two letters are uppercase). Indeed, I can't find
the word "codeML" (or "CodeML") in the PAML's documents.


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


On Sat, 16 Aug 2008 18:22:18 +0200
pjotr2008 at thebird.nl (Pjotr Prins) wrote:

> codeml is, by far, the most valuable tool.
> 
> Pj.
> 
> On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> > Hi Mike,
> > 
> > The CodeML wrappers is now included in bioruby git.
> > http://github.com/bioruby/bioruby/tree/master
> > 
> > As PAML has some executables other than codeml,
> > (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> > I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> > files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> > 
> > Is it OK? (or, is codeml the only valuable component to write
> > wrapper/parser for bioruby?)
> > 
> > Do you (or someone) plan to write other PAML's wrappers/parsers?
> > 
> > Thanks,
> > 
> > Naohisa Goto
> > ngoto at bioruby.org / ng at bioruby.org
> > 
> > 
> > On Fri, 15 Aug 2008 20:15:09 +0900
> > Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> > 
> > > Hi, 
> > > 
> > > It seems good. It will be included in BioRuby.
> > > 
> > > In my machine, a test was failed.
> > > Can you fix the problem?
> > (snip)
> > >
> > > On Wed, 13 Aug 2008 16:34:20 +0100
> > > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > > 
> > > > Hi,
> > > > 
> > > > CodeML is a common tool for estimating evolutionary rate of protein encoding
> > > > sequences, and is part of the PAML package. I've created a codeml wrapper
> > > > and two parsers. Unit tests are also included. The code is in a Github fork
> > > > in BioRuby. The fork is located here
> > > > 
> > > > http://github.com/michaelbarton/bioruby/tree/master
> > > > 
> > > > I like to suggested that it for inclusion in the main BioRuby branch.
> > > > 
> > > > Thanks
> > > > 
> > > > Mike
> > > > _______________________________________________

From mail at michaelbarton.me.uk  Mon Aug 18 07:06:08 2008
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Mon, 18 Aug 2008 12:06:08 +0100
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
	<20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
	<20080816162218.GA4512@thebird.nl>
	<20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <c27b73c0808180406q647c353eg51e5ebcdff8f6dd4@mail.gmail.com>

Naohisa thank you for the effort you have made in correcting the code to
work with the rest of BioRuby.
I agree that Codeml should be the correct name for the class. I also agree
that Bio::PAML::Codeml is a sensible naming structure so that the other PAML
tools can be included.

I will attempt to fix the bugs you have highlighted over the next week. I
have no plans to write parsers for the other PAML tools as codeml is the
only one I am currently using at the moment.

Thanks

Mike

On Mon, Aug 18, 2008 at 7:18 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Thank you.
>
> I think PAML programs other than codeml are also valuale
> to write wrappers, especially for baseml and yn00.
>
> In BioPerl, there are four PAML program wrappers.
> (baseml, codeml, evolver, yn00)
>
> http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML
>
> So, I decide to move the codeml classes under Bio::PAML.
>
> I renamed Bio::CodeML to Bio::PAML::Codeml. Files are moved
> to bio/appl/paml/ and test/unit/bio/appl/paml/.
>
> The reason why I changed CodeML to Codeml is that
> it seems that authors of PAML do not use the word "codeML"
> (the last two letters are uppercase). Indeed, I can't find
> the word "codeML" (or "CodeML") in the PAML's documents.
>
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
>
> On Sat, 16 Aug 2008 18:22:18 +0200
> pjotr2008 at thebird.nl (Pjotr Prins) wrote:
>
> > codeml is, by far, the most valuable tool.
> >
> > Pj.
> >
> > On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> > > Hi Mike,
> > >
> > > The CodeML wrappers is now included in bioruby git.
> > > http://github.com/bioruby/bioruby/tree/master
> > >
> > > As PAML has some executables other than codeml,
> > > (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> > > I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> > > files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> > >
> > > Is it OK? (or, is codeml the only valuable component to write
> > > wrapper/parser for bioruby?)
> > >
> > > Do you (or someone) plan to write other PAML's wrappers/parsers?
> > >
> > > Thanks,
> > >
> > > Naohisa Goto
> > > ngoto at bioruby.org / ng at bioruby.org
> > >
> > >
> > > On Fri, 15 Aug 2008 20:15:09 +0900
> > > Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> > >
> > > > Hi,
> > > >
> > > > It seems good. It will be included in BioRuby.
> > > >
> > > > In my machine, a test was failed.
> > > > Can you fix the problem?
> > > (snip)
> > > >
> > > > On Wed, 13 Aug 2008 16:34:20 +0100
> > > > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > CodeML is a common tool for estimating evolutionary rate of protein
> encoding
> > > > > sequences, and is part of the PAML package. I've created a codeml
> wrapper
> > > > > and two parsers. Unit tests are also included. The code is in a
> Github fork
> > > > > in BioRuby. The fork is located here
> > > > >
> > > > > http://github.com/michaelbarton/bioruby/tree/master
> > > > >
> > > > > I like to suggested that it for inclusion in the main BioRuby
> branch.
> > > > >
> > > > > Thanks
> > > > >
> > > > > Mike
> > > > > _______________________________________________
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

From mail at michaelbarton.me.uk  Tue Aug 19 09:52:43 2008
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Tue, 19 Aug 2008 14:52:43 +0100
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
	<20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
	<20080816162218.GA4512@thebird.nl>
	<20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <c27b73c0808190652i5fc9fef2l94ee31290cf545bc@mail.gmail.com>

Hi,

I've updated the Bio::PAML::Codeml::Rates class to pasrse columns with the
'*', which indicate gaps in the alignment. For instance MM*M means that
there is a gap in the alignment in the third sequence.

The changes are in my branch of bioruby.

Thanks

Mike

On Mon, Aug 18, 2008 at 7:18 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Thank you.
>
> I think PAML programs other than codeml are also valuale
> to write wrappers, especially for baseml and yn00.
>
> In BioPerl, there are four PAML program wrappers.
> (baseml, codeml, evolver, yn00)
>
> http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML
>
> So, I decide to move the codeml classes under Bio::PAML.
>
> I renamed Bio::CodeML to Bio::PAML::Codeml. Files are moved
> to bio/appl/paml/ and test/unit/bio/appl/paml/.
>
> The reason why I changed CodeML to Codeml is that
> it seems that authors of PAML do not use the word "codeML"
> (the last two letters are uppercase). Indeed, I can't find
> the word "codeML" (or "CodeML") in the PAML's documents.
>
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
>
> On Sat, 16 Aug 2008 18:22:18 +0200
> pjotr2008 at thebird.nl (Pjotr Prins) wrote:
>
> > codeml is, by far, the most valuable tool.
> >
> > Pj.
> >
> > On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> > > Hi Mike,
> > >
> > > The CodeML wrappers is now included in bioruby git.
> > > http://github.com/bioruby/bioruby/tree/master
> > >
> > > As PAML has some executables other than codeml,
> > > (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> > > I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> > > files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> > >
> > > Is it OK? (or, is codeml the only valuable component to write
> > > wrapper/parser for bioruby?)
> > >
> > > Do you (or someone) plan to write other PAML's wrappers/parsers?
> > >
> > > Thanks,
> > >
> > > Naohisa Goto
> > > ngoto at bioruby.org / ng at bioruby.org
> > >
> > >
> > > On Fri, 15 Aug 2008 20:15:09 +0900
> > > Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> > >
> > > > Hi,
> > > >
> > > > It seems good. It will be included in BioRuby.
> > > >
> > > > In my machine, a test was failed.
> > > > Can you fix the problem?
> > > (snip)
> > > >
> > > > On Wed, 13 Aug 2008 16:34:20 +0100
> > > > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > CodeML is a common tool for estimating evolutionary rate of protein
> encoding
> > > > > sequences, and is part of the PAML package. I've created a codeml
> wrapper
> > > > > and two parsers. Unit tests are also included. The code is in a
> Github fork
> > > > > in BioRuby. The fork is located here
> > > > >
> > > > > http://github.com/michaelbarton/bioruby/tree/master
> > > > >
> > > > > I like to suggested that it for inclusion in the main BioRuby
> branch.
> > > > >
> > > > > Thanks
> > > > >
> > > > > Mike
> > > > > _______________________________________________
> _______________________________________________
> 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  Tue Aug 19 10:51:18 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 19 Aug 2008 23:51:18 +0900
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <c27b73c0808190652i5fc9fef2l94ee31290cf545bc@mail.gmail.com>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
	<20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
	<20080816162218.GA4512@thebird.nl>
	<20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>
	<c27b73c0808190652i5fc9fef2l94ee31290cf545bc@mail.gmail.com>
Message-ID: <20080819145119.E1D101CBC541@idnmail.gen-info.osaka-u.ac.jp>

Hi,

The changes are now included in bioruby git repository.
http://github.com/bioruby/bioruby/commits/master

Thanks for improvement.

In addition, changes for Blast classes made by me
(already appeared in github.com/ngoto/bioruby) are
also included now.

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

On Tue, 19 Aug 2008 14:52:43 +0100
"Michael Barton" <mail at michaelbarton.me.uk> wrote:

> Hi,
> 
> I've updated the Bio::PAML::Codeml::Rates class to pasrse columns with the
> '*', which indicate gaps in the alignment. For instance MM*M means that
> there is a gap in the alignment in the third sequence.
> 
> The changes are in my branch of bioruby.
> 
> Thanks
> 
> Mike
> 
> On Mon, Aug 18, 2008 at 7:18 AM, Naohisa GOTO
> <ngoto at gen-info.osaka-u.ac.jp>wrote:
> 
> > Thank you.
> >
> > I think PAML programs other than codeml are also valuale
> > to write wrappers, especially for baseml and yn00.
> >
> > In BioPerl, there are four PAML program wrappers.
> > (baseml, codeml, evolver, yn00)
> >
> > http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML
> >
> > So, I decide to move the codeml classes under Bio::PAML.
> >
> > I renamed Bio::CodeML to Bio::PAML::Codeml. Files are moved
> > to bio/appl/paml/ and test/unit/bio/appl/paml/.
> >
> > The reason why I changed CodeML to Codeml is that
> > it seems that authors of PAML do not use the word "codeML"
> > (the last two letters are uppercase). Indeed, I can't find
> > the word "codeML" (or "CodeML") in the PAML's documents.
> >
> >
> > Naohisa Goto
> > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> >
> >
> > On Sat, 16 Aug 2008 18:22:18 +0200
> > pjotr2008 at thebird.nl (Pjotr Prins) wrote:
> >
> > > codeml is, by far, the most valuable tool.
> > >
> > > Pj.
> > >
> > > On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> > > > Hi Mike,
> > > >
> > > > The CodeML wrappers is now included in bioruby git.
> > > > http://github.com/bioruby/bioruby/tree/master
> > > >
> > > > As PAML has some executables other than codeml,
> > > > (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> > > > I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> > > > files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> > > >
> > > > Is it OK? (or, is codeml the only valuable component to write
> > > > wrapper/parser for bioruby?)
> > > >
> > > > Do you (or someone) plan to write other PAML's wrappers/parsers?
> > > >
> > > > Thanks,
> > > >
> > > > Naohisa Goto
> > > > ngoto at bioruby.org / ng at bioruby.org
> > > >
> > > >
> > > > On Fri, 15 Aug 2008 20:15:09 +0900
> > > > Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > It seems good. It will be included in BioRuby.
> > > > >
> > > > > In my machine, a test was failed.
> > > > > Can you fix the problem?
> > > > (snip)
> > > > >
> > > > > On Wed, 13 Aug 2008 16:34:20 +0100
> > > > > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > CodeML is a common tool for estimating evolutionary rate of protein
> > encoding
> > > > > > sequences, and is part of the PAML package. I've created a codeml
> > wrapper
> > > > > > and two parsers. Unit tests are also included. The code is in a
> > Github fork
> > > > > > in BioRuby. The fork is located here
> > > > > >
> > > > > > http://github.com/michaelbarton/bioruby/tree/master
> > > > > >
> > > > > > I like to suggested that it for inclusion in the main BioRuby
> > branch.
> > > > > >
> > > > > > Thanks
> > > > > >
> > > > > > Mike
> > > > > > _______________________________________________
> > _______________________________________________
> > 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 davide.rambaldi at ifom-ieo-campus.it  Fri Aug 29 10:44:13 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Fri, 29 Aug 2008 16:44:13 +0200
Subject: [BioRuby] test and bioruby shell questions
Message-ID: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>

Greetings,
  I am a new user of ruby and bioruby and I really like it especially  
for the opportunity to test interactively with irb and BioRuby shell

  I have some question please:

- TESTING (bioruby 1.2.1 and ruby 1.8.7 on a Power PC G4 osx)
   during testing

  I got 7 errors:

  	test_gff_exportview(Bio::FuncTestEnsemblHuman) [./functional/bio/ 
io/test_ensembl.rb:95]:
	test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./ 
functional/bio/io/test_ensembl.rb:121]:
	test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./ 
functional/bio/io/test_ensembl.rb:180]:
	test_list_falsenegative(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1304]:
	test_list_falsepositive(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1356]:
	test_list_potentialhit(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1408]:
	test_list_truepositive(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1236]:

   Is a know problem or related with my computer?


- BioRuby SHELL
   during shell demo (demo command) there is a crash after:
kuma = getobj("gb:AF237819")
Retrieving entry from KEGG API (gb:AF237819)
   ==> nil
bioruby> kuma.definition
NoMethodError: undefined method `definition' for nil:NilClass
         from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in  
`irb_binding'
         from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in  
`irb_binding'
         from /usr/local/lib/ruby/1.8/irb/workspace.rb:52
Maybe IRB bug!!

   crash because kuma is empty? irb can reach the sequence?
bioruby> kuma
   ==> nil


- SHELL OBJECTS and HELP

   there is a way to delete shell objects (.bioruby/shell/session/ 
object) directly from the shell?
   a "rm" command?
   there is an help in the BioRuby shell? (help give me => nil,  ./ 
bioruby --help give unrecognized option )


Thanks and 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 donttrustben at gmail.com  Sat Aug 30 07:13:32 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Sat, 30 Aug 2008 21:13:32 +1000
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
Message-ID: <bb2b67d00808300413h4fca205bo84fad43b487a211@mail.gmail.com>

Hi,

Using the edge version of bioruby I get 7 errors as well, although
they are slightly different. I wouldn't be too worried.

$ ruby runner.rb
Loaded suite .
Started
.....FF..F.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
Finished in 133.52153 seconds.

  1) Failure:
test_gff_exportview(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:95]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  2) Failure:
test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:121]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  3) Failure:
test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:180]:
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tENSG00000206158\tENST00000382964\tENSE00001494097\tKNOWN_protein_coding\n">
expected but was
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n">.

  4) Failure:
test_id_line_sequence_version(Bio::TestEMBL)
[./unit/bio/db/embl/test_embl_rel89.rb:45]:
<"1"> expected but was
<nil>.

  5) Failure:
test_left_padding(Bio::TestStringFormatting)
[./unit/bio/util/restriction_enzyme/test_string_formatting.rb:43]:
<"nnnnnnn"> expected but was
<"">.

  6) Failure:
test_right_padding(Bio::TestStringFormatting)
[./unit/bio/util/restriction_enzyme/test_string_formatting.rb:50]:
<"nn"> expected but was
<"">.

  7) Error:
test_strip_padding(Bio::TestStringFormatting):
NoMethodError: undefined method `[]' for nil:NilClass
    ../lib/bio/util/restriction_enzyme/string_formatting.rb:64:in
`strip_padding'
    ./unit/bio/util/restriction_enzyme/test_string_formatting.rb:33:in
`test_strip_padding'

1867 tests, 4049 assertions, 6 failures, 1 errors






Can't help with the bioruby shell, sorry, as I don't use it. Why would
you want to remove objects, though?

Thanks,
ben

2008/8/30 Davide Rambaldi <davide.rambaldi at ifom-ieo-campus.it>:
> Greetings,
>  I am a new user of ruby and bioruby and I really like it especially for the
> opportunity to test interactively with irb and BioRuby shell
>
>  I have some question please:
>
> - TESTING (bioruby 1.2.1 and ruby 1.8.7 on a Power PC G4 osx)
>  during testing
>
>  I got 7 errors:
>
>        test_gff_exportview(Bio::FuncTestEnsemblHuman)
> [./functional/bio/io/test_ensembl.rb:95]:
>        test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
> [./functional/bio/io/test_ensembl.rb:121]:
>        test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
> [./functional/bio/io/test_ensembl.rb:180]:
>        test_list_falsenegative(Bio::TestPROSITE)
> [./unit/bio/db/test_prosite.rb:1304]:
>        test_list_falsepositive(Bio::TestPROSITE)
> [./unit/bio/db/test_prosite.rb:1356]:
>        test_list_potentialhit(Bio::TestPROSITE)
> [./unit/bio/db/test_prosite.rb:1408]:
>        test_list_truepositive(Bio::TestPROSITE)
> [./unit/bio/db/test_prosite.rb:1236]:
>
>  Is a know problem or related with my computer?
>
>
> - BioRuby SHELL
>  during shell demo (demo command) there is a crash after:
> kuma = getobj("gb:AF237819")
> Retrieving entry from KEGG API (gb:AF237819)
>  ==> nil
> bioruby> kuma.definition
> NoMethodError: undefined method `definition' for nil:NilClass
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in `irb_binding'
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in `irb_binding'
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52
> Maybe IRB bug!!
>
>  crash because kuma is empty? irb can reach the sequence?
> bioruby> kuma
>  ==> nil
>
>
> - SHELL OBJECTS and HELP
>
>  there is a way to delete shell objects (.bioruby/shell/session/object)
> directly from the shell?
>  a "rm" command?
>  there is an help in the BioRuby shell? (help give me => nil,  ./bioruby
> --help give unrecognized option )
>
>
> Thanks and 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)
>
> -----------------------------------------------------
>
>
>
>
> _______________________________________________
> 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 ktym at hgc.jp  Sat Aug 30 08:16:01 2008
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Sat, 30 Aug 2008 21:16:01 +0900
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
Message-ID: <992DF6FE-14DF-45B9-B141-224FF473E82B@hgc.jp>

Dear Davide,

On 2008/08/29, at 23:44, Davide Rambaldi wrote:
> - BioRuby SHELL
>  during shell demo (demo command) there is a crash after:
> kuma = getobj("gb:AF237819")
> Retrieving entry from KEGG API (gb:AF237819)
>  ==> nil
> bioruby> kuma.definition
> NoMethodError: undefined method `definition' for nil:NilClass
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in `irb_binding'
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in `irb_binding'
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52
> Maybe IRB bug!!
>
>  crash because kuma is empty? irb can reach the sequence?
> bioruby> kuma
>  ==> nil

This feature (obtaining GenBank entry by getobj method) is temporally unavailable
because of the discontinuation of the GenBank retrieval service in KEGG API
developed at the Kyoto University in Japan.

The demo above was designed to utilize the KEGG API, which is a SOAP based web service,
so we need to change the default data source to obtain this entry.
We can fix this by switching to use NCBI's efetch method instead.


> - SHELL OBJECTS and HELP
>
>  there is a way to delete shell objects (.bioruby/shell/session/object) directly from the shell?
>  a "rm" command?

Yes.

If you have a large object which you don't want to save persistently over the sessions,

bioruby> a = "atgc" * 10000

you can remove it by the name of the variable

bioruby> rm "a"

or by the symbol of the variable name

bioruby> rm :a

Actually, the rm command temporally assign 'nil' to the variable
because BioRuby shell will avoid to dump variables having 'nil' as its value.
(This means, the memory will not be returned to the OS until next GC.)

This implementation looks somewhat ugly, so if you have a better idea, please let me know.


>  there is an help in the BioRuby shell? (help give me => nil,  ./bioruby --help give unrecognized option )

Planned but never implemented. Sorry.

Regards,
Toshiaki Katayama




From ngoto at gen-info.osaka-u.ac.jp  Sun Aug 31 00:05:52 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sun, 31 Aug 2008 13:05:52 +0900
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
Message-ID: <20080831040553.5381A1CBC3AF@idnmail.gen-info.osaka-u.ac.jp>

Hi,

Thank you for reporting.

On Fri, 29 Aug 2008 16:44:13 +0200
Davide Rambaldi <davide.rambaldi at ifom-ieo-campus.it> wrote:

> Greetings,
>   I am a new user of ruby and bioruby and I really like it especially  
> for the opportunity to test interactively with irb and BioRuby shell
> 
>   I have some question please:
> 
> - TESTING (bioruby 1.2.1 and ruby 1.8.7 on a Power PC G4 osx)
>    during testing
> 
>   I got 7 errors:
> 
>   	test_gff_exportview(Bio::FuncTestEnsemblHuman) [./functional/bio/ 
> io/test_ensembl.rb:95]:
> 	test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./ 
> functional/bio/io/test_ensembl.rb:121]:
> 	test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./ 
> functional/bio/io/test_ensembl.rb:180]:

Next time, please show all failure message, even if long.

Perhaps they are caused by the change of the Ensembl.
For a reminder, I submitted to the bug tracking system of BioRuby.
http://rubyforge.org/tracker/index.php?func=detail&aid=21744&group_id=769&atid=3037

> 	test_list_falsenegative(Bio::TestPROSITE) [./unit/bio/db/ 
> test_prosite.rb:1304]:
> 	test_list_falsepositive(Bio::TestPROSITE) [./unit/bio/db/ 
> test_prosite.rb:1356]:
> 	test_list_potentialhit(Bio::TestPROSITE) [./unit/bio/db/ 
> test_prosite.rb:1408]:
> 	test_list_truepositive(Bio::TestPROSITE) [./unit/bio/db/ 
> test_prosite.rb:1236]:

These are caused by changes of order of data in arrays, due to
the change of hash algorithm in Ruby 1.8.7 (and in Ruby 1.9.0).

I fixed these tests not to affected by order of data.
This is already included in git repository.
http://github.com/bioruby/bioruby/commit/e86f8d757c45805389e154f06ccde5a3d9e8a557

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

From ngoto at gen-info.osaka-u.ac.jp  Sun Aug 31 00:25:46 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sun, 31 Aug 2008 13:25:46 +0900
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <bb2b67d00808300413h4fca205bo84fad43b487a211@mail.gmail.com>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<bb2b67d00808300413h4fca205bo84fad43b487a211@mail.gmail.com>
Message-ID: <20080831042546.D246F1CBC56E@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Sat, 30 Aug 2008 21:13:32 +1000
"Ben Woodcroft" <donttrustben at gmail.com> wrote:

> Hi,
> 
> Using the edge version of bioruby I get 7 errors as well, although
> they are slightly different. I wouldn't be too worried.

What BioRuby version, Ruby version, and OS and CPU did you use?

> 
> $ ruby runner.rb
> Loaded suite .
> Started
> .....FF..F..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 .!
>  ..............................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
> Finished in 133.52153 seconds.
> 
  1) Failure:
test_gff_exportview(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:95]:
(snip)

1) to 3) seems the same as the previous mail.
http://rubyforge.org/tracker/index.php?func=detail&aid=21744&group_id=769&atid=3037
This still remains unfixed.

>   4) Failure:
> test_id_line_sequence_version(Bio::TestEMBL)
> [./unit/bio/db/embl/test_embl_rel89.rb:45]:
> <"1"> expected but was
> <nil>.

I see this first time.
Which bioruby version?

>   5) Failure:
> test_left_padding(Bio::TestStringFormatting)
> [./unit/bio/util/restriction_enzyme/test_string_formatting.rb:43]:
> <"nnnnnnn"> expected but was
> <"">.
> 
>   6) Failure:
> test_right_padding(Bio::TestStringFormatting)
> [./unit/bio/util/restriction_enzyme/test_string_formatting.rb:50]:
> <"nn"> expected but was
> <"">.
> 
>   7) Error:
> test_strip_padding(Bio::TestStringFormatting):
> NoMethodError: undefined method `[]' for nil:NilClass
>     ../lib/bio/util/restriction_enzyme/string_formatting.rb:64:in
> `strip_padding'
>     ./unit/bio/util/restriction_enzyme/test_string_formatting.rb:33:in
> `test_strip_padding'
> 
> 1867 tests, 4049 assertions, 6 failures, 1 errors
> 

I believe commit 735e3563b723645afa65f0e4213a7c92152f68ec
fixed 5) to 7).

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

From donttrustben at gmail.com  Sun Aug 31 03:11:31 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Sun, 31 Aug 2008 17:11:31 +1000
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <20080831042546.D246F1CBC56E@idnmail.gen-info.osaka-u.ac.jp>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<bb2b67d00808300413h4fca205bo84fad43b487a211@mail.gmail.com>
	<20080831042546.D246F1CBC56E@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <bb2b67d00808310011p7232608dk645434272f729e4b@mail.gmail.com>

Hi,

Thanks for your concern.
After pulling from the newest github -
http://github.com/bioruby/bioruby/commit/e86f8d757c45805389e154f06ccde5a3d9e8a557

$ ruby -v
ruby 1.8.6 (2007-09-24 patchlevel 111) [i486-linux]
$ uname -a
Linux uyen 2.6.24-21-generic #1 SMP Mon Aug 25 17:32:09 UTC 2008 i686 GNU/Linux

Using Ubuntu Hardy, and the latest patched version of the ruby1.8
package (1.8.6.111-2ubuntu1.1)

$ ruby runner.rb
Loaded suite .
Started
.....FF..F.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
Finished in 142.816902 seconds.

  1) Failure:
test_gff_exportview(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:95]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  2) Failure:
test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:121]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  3) Failure:
test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:180]:
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tENSG00000206158\tENST00000382964\tENSE00001494097\tKNOWN_protein_coding\n">
expected but was
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n">.

  4) Failure:
test_id_line_sequence_version(Bio::TestEMBL)
[./unit/bio/db/embl/test_embl_rel89.rb:45]:
<"1"> expected but was
<nil>.

  5) Failure:
test_left_padding(Bio::TestStringFormatting)
[./unit/bio/util/restriction_enzyme/test_string_formatting.rb:43]:
<"nnnnnnn"> expected but was
<"">.

  6) Failure:
test_right_padding(Bio::TestStringFormatting)
[./unit/bio/util/restriction_enzyme/test_string_formatting.rb:50]:
<"nn"> expected but was
<"">.

  7) Error:
test_strip_padding(Bio::TestStringFormatting):
NoMethodError: undefined method `[]' for nil:NilClass
    ../lib/bio/util/restriction_enzyme/string_formatting.rb:64:in
`strip_padding'
    ./unit/bio/util/restriction_enzyme/test_string_formatting.rb:33:in
`test_strip_padding'

1867 tests, 4049 assertions, 6 failures, 1 errors

I don't actually care personally about these problems, but am glad to
help out in a general sense.

Thanks,
ben



2008/8/31 Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp>:
> Hi,
>
> On Sat, 30 Aug 2008 21:13:32 +1000
> "Ben Woodcroft" <donttrustben at gmail.com> wrote:
>
>> Hi,
>>
>> Using the edge version of bioruby I get 7 errors as well, although
>> they are slightly different. I wouldn't be too worried.
>
> What BioRuby version, Ruby version, and OS and CPU did you use?
>
>>
>> $ ruby runner.rb
>> Loaded suite .
>> Started
>> .....FF..F..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
>  .!
>>  ..............................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
>> Finished in 133.52153 seconds.
>>
>  1) Failure:
> test_gff_exportview(Bio::FuncTestEnsemblHuman)
> [./functional/bio/io/test_ensembl.rb:95]:
> (snip)
>
> 1) to 3) seems the same as the previous mail.
> http://rubyforge.org/tracker/index.php?func=detail&aid=21744&group_id=769&atid=3037
> This still remains unfixed.
>
>>   4) Failure:
>> test_id_line_sequence_version(Bio::TestEMBL)
>> [./unit/bio/db/embl/test_embl_rel89.rb:45]:
>> <"1"> expected but was
>> <nil>.
>
> I see this first time.
> Which bioruby version?
>
>>   5) Failure:
>> test_left_padding(Bio::TestStringFormatting)
>> [./unit/bio/util/restriction_enzyme/test_string_formatting.rb:43]:
>> <"nnnnnnn"> expected but was
>> <"">.
>>
>>   6) Failure:
>> test_right_padding(Bio::TestStringFormatting)
>> [./unit/bio/util/restriction_enzyme/test_string_formatting.rb:50]:
>> <"nn"> expected but was
>> <"">.
>>
>>   7) Error:
>> test_strip_padding(Bio::TestStringFormatting):
>> NoMethodError: undefined method `[]' for nil:NilClass
>>     ../lib/bio/util/restriction_enzyme/string_formatting.rb:64:in
>> `strip_padding'
>>     ./unit/bio/util/restriction_enzyme/test_string_formatting.rb:33:in
>> `test_strip_padding'
>>
>> 1867 tests, 4049 assertions, 6 failures, 1 errors
>>
>
> I believe commit 735e3563b723645afa65f0e4213a7c92152f68ec
> fixed 5) to 7).
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> _______________________________________________
> 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 mail at michaelbarton.me.uk  Thu Aug  7 15:20:23 2008
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Thu, 7 Aug 2008 16:20:23 +0100
Subject: [BioRuby] Problem with autoload in lib/bio.rb
Message-ID: <c27b73c0808070820n45a90cdaia917ff974927ec46@mail.gmail.com>

Hello,

I'm currently having some problems trying to use BioRuby from the source.
Specifically I'm having problems try to access some of the applications
defined using autoload in irb.

For example

> require 'lib/bio'
> Bio::Iprscan
LoadError: no such file to load -- bio/appl/iprscan/report
    from (irb):4

Could anyone provide a suggestion as to what I'm doing wrong? I'm some what
stuck at this point.

Thanks

Mike


From pjotr2008 at thebird.nl  Thu Aug  7 15:30:44 2008
From: pjotr2008 at thebird.nl (Pjotr Prins)
Date: Thu, 7 Aug 2008 17:30:44 +0200
Subject: [BioRuby] Problem with autoload in lib/bio.rb
In-Reply-To: <c27b73c0808070820n45a90cdaia917ff974927ec46@mail.gmail.com>
References: <c27b73c0808070820n45a90cdaia917ff974927ec46@mail.gmail.com>
Message-ID: <20080807153044.GA28970@thebird.nl>

Are you giving an include path (-I with ruby, or RUBYLIB environment
variable)? In irb you may be able to do:

$: << 'pathtobioruby/bioruby/lib'
require 'bio'


On Thu, Aug 07, 2008 at 04:20:23PM +0100, Michael Barton wrote:
> Hello,
> 
> I'm currently having some problems trying to use BioRuby from the source.
> Specifically I'm having problems try to access some of the applications
> defined using autoload in irb.
> 
> For example
> 
> > require 'lib/bio'
> > Bio::Iprscan
> LoadError: no such file to load -- bio/appl/iprscan/report
>     from (irb):4
> 
> Could anyone provide a suggestion as to what I'm doing wrong? I'm some what
> stuck at this point.
> 
> Thanks
> 
> Mike
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From mail at michaelbarton.me.uk  Fri Aug  8 14:02:09 2008
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Fri, 8 Aug 2008 15:02:09 +0100
Subject: [BioRuby] Problem with autoload in lib/bio.rb
In-Reply-To: <20080807153044.GA28970@thebird.nl>
References: <c27b73c0808070820n45a90cdaia917ff974927ec46@mail.gmail.com>
	<20080807153044.GA28970@thebird.nl>
Message-ID: <c27b73c0808080702t1097a842lcc64249ab2690c28@mail.gmail.com>

Thanks Pjotr, that works. I'm having some trouble getting something similar
to work with active_resource though, where I have to explicitly require each
app.

For example

require 'bio'
require 'bio/appl/iprscan'

I wonder if you have ever come across something like this before?

Thanks

Mike


On Thu, Aug 7, 2008 at 4:30 PM, Pjotr Prins <pjotr2008 at thebird.nl> wrote:

> Are you giving an include path (-I with ruby, or RUBYLIB environment
> variable)? In irb you may be able to do:
>
> $: << 'pathtobioruby/bioruby/lib'
> require 'bio'
>
>
> On Thu, Aug 07, 2008 at 04:20:23PM +0100, Michael Barton wrote:
> > Hello,
> >
> > I'm currently having some problems trying to use BioRuby from the source.
> > Specifically I'm having problems try to access some of the applications
> > defined using autoload in irb.
> >
> > For example
> >
> > > require 'lib/bio'
> > > Bio::Iprscan
> > LoadError: no such file to load -- bio/appl/iprscan/report
> >     from (irb):4
> >
> > Could anyone provide a suggestion as to what I'm doing wrong? I'm some
> what
> > stuck at this point.
> >
> > Thanks
> >
> > Mike
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>


From gtraub at flmnh.ufl.edu  Tue Aug 12 18:09:56 2008
From: gtraub at flmnh.ufl.edu (Greg Traub)
Date: Tue, 12 Aug 2008 14:09:56 -0400
Subject: [BioRuby] Help with Bio::Blast
Message-ID: <48A1D1F4.5040704@flmnh.ufl.edu>

Hello,

I'm new to BioRuby but not new to Ruby. I've been trying to write code 
to submit a fasta formated sequence for BLAST search, however I never 
get back anything thats usable. After reading the documentation, I 
should be receiving xml formated responses to my search, but I dont 
receive anything. I altered the code in Bio::Blast class to print out 
whatever raw data was being sent back from my request and to my 
surprise, I keep receiving standard formated HTML page that tells me my 
request is either requesting the wrong program or the wrong database . 
I've been trying to use 'blastn' with 'nr' or 'nr-nt' ...documentation 
seems differ as to what the name of the databases are, so I've tried all 
of them with no luck. Now what really gets me is that i should be 
getting back XML. I would even an expect the error message to be in XML 
but instead its in a  HTML page  with javascript included.  This makes 
me think that the request is going to URL not intended for XML 
responses. Can anybody help me?  I've pasted some example code that I've 
tried below.

Thanks,
Greg

#files is array of file locations
#res is response
#im just trying to get back any info i can from the request
#in the example code below

blast = Bio::Blast.remote('blastn','nr')
files.each do |file|
     Bio::FastaFormat.open(file).each_entry do |c|
        reports = blast.query(c.seq)
        reports.each { |report| res << report.query_seq }
     end
end

-- 
Database Programmer
Florida Museum of Natural History
University of Florida
gtraub at flmnh.ufl.edu
(352) 392-1721 ext. 514
----------------------------------

Experience is what you get when
you didn't get what you want.
-National Vacuum sign



From donttrustben at gmail.com  Wed Aug 13 03:59:03 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Wed, 13 Aug 2008 13:59:03 +1000
Subject: [BioRuby] Help with Bio::Blast
In-Reply-To: <48A1D1F4.5040704@flmnh.ufl.edu>
References: <48A1D1F4.5040704@flmnh.ufl.edu>
Message-ID: <bb2b67d00808122059s77b7b142od69ff3085e2181d4@mail.gmail.com>

I don't personally use the bioruby blast interface because I'm more
used to the plain old blast command line interface, but I can suggest
a workaround. What if you just put '-m 7' (ie blast output) in the
options?

The only other problem is that the new version of blast XML isn't well
supported by bioruby. Read the bug report for more information:
http://rubyforge.org/tracker/index.php?func=detail&aid=20272&group_id=769&atid=3037

Thanks,
ben

2008/8/13 Greg Traub <gtraub at flmnh.ufl.edu>:
> Hello,
>
> I'm new to BioRuby but not new to Ruby. I've been trying to write code to
> submit a fasta formated sequence for BLAST search, however I never get back
> anything thats usable. After reading the documentation, I should be
> receiving xml formated responses to my search, but I dont receive anything.
> I altered the code in Bio::Blast class to print out whatever raw data was
> being sent back from my request and to my surprise, I keep receiving
> standard formated HTML page that tells me my request is either requesting
> the wrong program or the wrong database . I've been trying to use 'blastn'
> with 'nr' or 'nr-nt' ...documentation seems differ as to what the name of
> the databases are, so I've tried all of them with no luck. Now what really
> gets me is that i should be getting back XML. I would even an expect the
> error message to be in XML but instead its in a  HTML page  with javascript
> included.  This makes me think that the request is going to URL not intended
> for XML responses. Can anybody help me?  I've pasted some example code that
> I've tried below.
>
> Thanks,
> Greg
>
> #files is array of file locations
> #res is response
> #im just trying to get back any info i can from the request
> #in the example code below
>
> blast = Bio::Blast.remote('blastn','nr')
> files.each do |file|
>    Bio::FastaFormat.open(file).each_entry do |c|
>       reports = blast.query(c.seq)
>       reports.each { |report| res << report.query_seq }
>    end
> end
>
> --
> Database Programmer
> Florida Museum of Natural History
> University of Florida
> gtraub at flmnh.ufl.edu
> (352) 392-1721 ext. 514
> ----------------------------------
>
> Experience is what you get when
> you didn't get what you want.
> -National Vacuum sign
>
> _______________________________________________
> 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 ngoto at gen-info.osaka-u.ac.jp  Wed Aug 13 03:53:17 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Wed, 13 Aug 2008 12:53:17 +0900
Subject: [BioRuby] Help with Bio::Blast
In-Reply-To: <48A1D1F4.5040704@flmnh.ufl.edu>
References: <48A1D1F4.5040704@flmnh.ufl.edu>
Message-ID: <20080813035317.A46F11CBC3C3@idnmail.gen-info.osaka-u.ac.jp>

Hello,

Related topic: 
http://lists.open-bio.org/pipermail/bioruby/2008-July/000664.html

I modified your code below.
However, because of the change of the behavior of remote site
(http://blast.genome.jp/), it may not work with long query sequences.

  res = []
  blast = Bio::Blast.remote('blastn', 'nr-nt', '-e 0.1')
  files.each do |file|
     Bio::FlatFile.foreach(Bio::FastaFormat, file) do |c|
        reports = blast.query(c.naseq.to_fasta(c.definition, 70))
        reports.each { |report| res << report.query_seq }
     end
  end

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

On Tue, 12 Aug 2008 14:09:56 -0400
Greg Traub <gtraub at flmnh.ufl.edu> wrote:

> Hello,
> 
> I'm new to BioRuby but not new to Ruby. I've been trying to write code 
> to submit a fasta formated sequence for BLAST search, however I never 
> get back anything thats usable. After reading the documentation, I 
> should be receiving xml formated responses to my search, but I dont 
> receive anything. I altered the code in Bio::Blast class to print out 
> whatever raw data was being sent back from my request and to my 
> surprise, I keep receiving standard formated HTML page that tells me my 
> request is either requesting the wrong program or the wrong database . 
> I've been trying to use 'blastn' with 'nr' or 'nr-nt' ...documentation 
> seems differ as to what the name of the databases are, so I've tried all 
> of them with no luck. Now what really gets me is that i should be 
> getting back XML. I would even an expect the error message to be in XML 
> but instead its in a  HTML page  with javascript included.  This makes 
> me think that the request is going to URL not intended for XML 
> responses. Can anybody help me?  I've pasted some example code that I've 
> tried below.
> 
> Thanks,
> Greg
> 
> #files is array of file locations
> #res is response
> #im just trying to get back any info i can from the request
> #in the example code below
> 
> blast = Bio::Blast.remote('blastn','nr')
> files.each do |file|
>      Bio::FastaFormat.open(file).each_entry do |c|
>         reports = blast.query(c.seq)
>         reports.each { |report| res << report.query_seq }
>      end
> end
> 
> -- 
> Database Programmer
> Florida Museum of Natural History
> University of Florida
> gtraub at flmnh.ufl.edu
> (352) 392-1721 ext. 514
> ----------------------------------
> 
> Experience is what you get when
> you didn't get what you want.
> -National Vacuum sign
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From mail at michaelbarton.me.uk  Wed Aug 13 15:34:20 2008
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Wed, 13 Aug 2008 16:34:20 +0100
Subject: [BioRuby] CodeML wrapper for BioRuby
Message-ID: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>

Hi,

CodeML is a common tool for estimating evolutionary rate of protein encoding
sequences, and is part of the PAML package. I've created a codeml wrapper
and two parsers. Unit tests are also included. The code is in a Github fork
in BioRuby. The fork is located here

http://github.com/michaelbarton/bioruby/tree/master

I like to suggested that it for inclusion in the main BioRuby branch.

Thanks

Mike


From ngoto at gen-info.osaka-u.ac.jp  Fri Aug 15 11:15:09 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Fri, 15 Aug 2008 20:15:09 +0900
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
Message-ID: <20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>

Hi, 

It seems good. It will be included in BioRuby.

In my machine, a test was failed.
Can you fix the problem?
------------------------------------------------------------
$ ruby test/unit/bio/appl/test_codeml.rb
Loaded suite test/unit/bio/appl/test_codeml
Started
..F....
Finished in 0.032717 seconds.

  1) Failure:
test_correct_options_should_be_loaded(Bio::TestConfigFileUsage) [test/unit/bio/appl/test_codeml.rb:87]:
<"/xxxxx/ngoto/work/test/data/codeml/abglobin.aa"> expected but was
<"/xxxxx/ngoto/work/bioruby/git/michaelbarton/bioruby/test/data/codeml/abglobin.aa">.

7 tests, 9 assertions, 1 failures, 0 errors
------------------------------------------------------------
(some part of file path is masked with "xxxxx")


On Wed, 13 Aug 2008 16:34:20 +0100
"Michael Barton" <mail at michaelbarton.me.uk> wrote:

> Hi,
> 
> CodeML is a common tool for estimating evolutionary rate of protein encoding
> sequences, and is part of the PAML package. I've created a codeml wrapper
> and two parsers. Unit tests are also included. The code is in a Github fork
> in BioRuby. The fork is located here
> 
> http://github.com/michaelbarton/bioruby/tree/master
> 
> I like to suggested that it for inclusion in the main BioRuby branch.
> 
> Thanks
> 
> Mike
> _______________________________________________
> 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  Sat Aug 16 08:45:21 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 16 Aug 2008 17:45:21 +0900
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>

Hi Mike,

The CodeML wrappers is now included in bioruby git.
http://github.com/bioruby/bioruby/tree/master

As PAML has some executables other than codeml,
(baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
I plan to move Bio::CodeML to Bio::PAML::CodeML, and
files are moved from bio/appl/codeml to bio/appl/paml/codeml.

Is it OK? (or, is codeml the only valuable component to write
wrapper/parser for bioruby?)

Do you (or someone) plan to write other PAML's wrappers/parsers?

Thanks,

Naohisa Goto
ngoto at bioruby.org / ng at bioruby.org


On Fri, 15 Aug 2008 20:15:09 +0900
Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:

> Hi, 
> 
> It seems good. It will be included in BioRuby.
> 
> In my machine, a test was failed.
> Can you fix the problem?
(snip)
>
> On Wed, 13 Aug 2008 16:34:20 +0100
> "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> 
> > Hi,
> > 
> > CodeML is a common tool for estimating evolutionary rate of protein encoding
> > sequences, and is part of the PAML package. I've created a codeml wrapper
> > and two parsers. Unit tests are also included. The code is in a Github fork
> > in BioRuby. The fork is located here
> > 
> > http://github.com/michaelbarton/bioruby/tree/master
> > 
> > I like to suggested that it for inclusion in the main BioRuby branch.
> > 
> > Thanks
> > 
> > Mike
> > _______________________________________________
> > 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


-- 
?? ??  ngoto at gen-info.osaka-u.ac.jp
??????????? ?????????? ?????????(???)
Phone: 06-6879-8365 / FAX: 06-6879-2047


From pjotr2008 at thebird.nl  Sat Aug 16 16:22:18 2008
From: pjotr2008 at thebird.nl (Pjotr Prins)
Date: Sat, 16 Aug 2008 18:22:18 +0200
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
	<20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <20080816162218.GA4512@thebird.nl>

codeml is, by far, the most valuable tool.

Pj.

On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> Hi Mike,
> 
> The CodeML wrappers is now included in bioruby git.
> http://github.com/bioruby/bioruby/tree/master
> 
> As PAML has some executables other than codeml,
> (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> 
> Is it OK? (or, is codeml the only valuable component to write
> wrapper/parser for bioruby?)
> 
> Do you (or someone) plan to write other PAML's wrappers/parsers?
> 
> Thanks,
> 
> Naohisa Goto
> ngoto at bioruby.org / ng at bioruby.org
> 
> 
> On Fri, 15 Aug 2008 20:15:09 +0900
> Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> 
> > Hi, 
> > 
> > It seems good. It will be included in BioRuby.
> > 
> > In my machine, a test was failed.
> > Can you fix the problem?
> (snip)
> >
> > On Wed, 13 Aug 2008 16:34:20 +0100
> > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > 
> > > Hi,
> > > 
> > > CodeML is a common tool for estimating evolutionary rate of protein encoding
> > > sequences, and is part of the PAML package. I've created a codeml wrapper
> > > and two parsers. Unit tests are also included. The code is in a Github fork
> > > in BioRuby. The fork is located here
> > > 
> > > http://github.com/michaelbarton/bioruby/tree/master
> > > 
> > > I like to suggested that it for inclusion in the main BioRuby branch.
> > > 
> > > Thanks
> > > 
> > > Mike
> > > _______________________________________________
> > > 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
> 
> 
> -- 
> ?$B8eF# ?$BD>5W  ngoto at gen-info.osaka-u.ac.jp
> ?$BBg:eBg3XHy at 8J*IB8&5f=j ?$B0dEA>pJs<B83%;%s%?!< ?$B%2%N%`>pJs2r at OJ,Ln(?$B0B1J8&)
> Phone: 06-6879-8365 / FAX: 06-6879-2047
> _______________________________________________
> 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 Aug 18 06:18:38 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 18 Aug 2008 15:18:38 +0900
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <20080816162218.GA4512@thebird.nl>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
	<20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
	<20080816162218.GA4512@thebird.nl>
Message-ID: <20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>

Thank you.

I think PAML programs other than codeml are also valuale
to write wrappers, especially for baseml and yn00.

In BioPerl, there are four PAML program wrappers.
(baseml, codeml, evolver, yn00)
http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML

So, I decide to move the codeml classes under Bio::PAML.  

I renamed Bio::CodeML to Bio::PAML::Codeml. Files are moved
to bio/appl/paml/ and test/unit/bio/appl/paml/.

The reason why I changed CodeML to Codeml is that
it seems that authors of PAML do not use the word "codeML"
(the last two letters are uppercase). Indeed, I can't find
the word "codeML" (or "CodeML") in the PAML's documents.


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


On Sat, 16 Aug 2008 18:22:18 +0200
pjotr2008 at thebird.nl (Pjotr Prins) wrote:

> codeml is, by far, the most valuable tool.
> 
> Pj.
> 
> On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> > Hi Mike,
> > 
> > The CodeML wrappers is now included in bioruby git.
> > http://github.com/bioruby/bioruby/tree/master
> > 
> > As PAML has some executables other than codeml,
> > (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> > I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> > files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> > 
> > Is it OK? (or, is codeml the only valuable component to write
> > wrapper/parser for bioruby?)
> > 
> > Do you (or someone) plan to write other PAML's wrappers/parsers?
> > 
> > Thanks,
> > 
> > Naohisa Goto
> > ngoto at bioruby.org / ng at bioruby.org
> > 
> > 
> > On Fri, 15 Aug 2008 20:15:09 +0900
> > Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> > 
> > > Hi, 
> > > 
> > > It seems good. It will be included in BioRuby.
> > > 
> > > In my machine, a test was failed.
> > > Can you fix the problem?
> > (snip)
> > >
> > > On Wed, 13 Aug 2008 16:34:20 +0100
> > > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > > 
> > > > Hi,
> > > > 
> > > > CodeML is a common tool for estimating evolutionary rate of protein encoding
> > > > sequences, and is part of the PAML package. I've created a codeml wrapper
> > > > and two parsers. Unit tests are also included. The code is in a Github fork
> > > > in BioRuby. The fork is located here
> > > > 
> > > > http://github.com/michaelbarton/bioruby/tree/master
> > > > 
> > > > I like to suggested that it for inclusion in the main BioRuby branch.
> > > > 
> > > > Thanks
> > > > 
> > > > Mike
> > > > _______________________________________________


From mail at michaelbarton.me.uk  Mon Aug 18 11:06:08 2008
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Mon, 18 Aug 2008 12:06:08 +0100
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
	<20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
	<20080816162218.GA4512@thebird.nl>
	<20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <c27b73c0808180406q647c353eg51e5ebcdff8f6dd4@mail.gmail.com>

Naohisa thank you for the effort you have made in correcting the code to
work with the rest of BioRuby.
I agree that Codeml should be the correct name for the class. I also agree
that Bio::PAML::Codeml is a sensible naming structure so that the other PAML
tools can be included.

I will attempt to fix the bugs you have highlighted over the next week. I
have no plans to write parsers for the other PAML tools as codeml is the
only one I am currently using at the moment.

Thanks

Mike

On Mon, Aug 18, 2008 at 7:18 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Thank you.
>
> I think PAML programs other than codeml are also valuale
> to write wrappers, especially for baseml and yn00.
>
> In BioPerl, there are four PAML program wrappers.
> (baseml, codeml, evolver, yn00)
>
> http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML
>
> So, I decide to move the codeml classes under Bio::PAML.
>
> I renamed Bio::CodeML to Bio::PAML::Codeml. Files are moved
> to bio/appl/paml/ and test/unit/bio/appl/paml/.
>
> The reason why I changed CodeML to Codeml is that
> it seems that authors of PAML do not use the word "codeML"
> (the last two letters are uppercase). Indeed, I can't find
> the word "codeML" (or "CodeML") in the PAML's documents.
>
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
>
> On Sat, 16 Aug 2008 18:22:18 +0200
> pjotr2008 at thebird.nl (Pjotr Prins) wrote:
>
> > codeml is, by far, the most valuable tool.
> >
> > Pj.
> >
> > On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> > > Hi Mike,
> > >
> > > The CodeML wrappers is now included in bioruby git.
> > > http://github.com/bioruby/bioruby/tree/master
> > >
> > > As PAML has some executables other than codeml,
> > > (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> > > I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> > > files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> > >
> > > Is it OK? (or, is codeml the only valuable component to write
> > > wrapper/parser for bioruby?)
> > >
> > > Do you (or someone) plan to write other PAML's wrappers/parsers?
> > >
> > > Thanks,
> > >
> > > Naohisa Goto
> > > ngoto at bioruby.org / ng at bioruby.org
> > >
> > >
> > > On Fri, 15 Aug 2008 20:15:09 +0900
> > > Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> > >
> > > > Hi,
> > > >
> > > > It seems good. It will be included in BioRuby.
> > > >
> > > > In my machine, a test was failed.
> > > > Can you fix the problem?
> > > (snip)
> > > >
> > > > On Wed, 13 Aug 2008 16:34:20 +0100
> > > > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > CodeML is a common tool for estimating evolutionary rate of protein
> encoding
> > > > > sequences, and is part of the PAML package. I've created a codeml
> wrapper
> > > > > and two parsers. Unit tests are also included. The code is in a
> Github fork
> > > > > in BioRuby. The fork is located here
> > > > >
> > > > > http://github.com/michaelbarton/bioruby/tree/master
> > > > >
> > > > > I like to suggested that it for inclusion in the main BioRuby
> branch.
> > > > >
> > > > > Thanks
> > > > >
> > > > > Mike
> > > > > _______________________________________________
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From mail at michaelbarton.me.uk  Tue Aug 19 13:52:43 2008
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Tue, 19 Aug 2008 14:52:43 +0100
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
	<20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
	<20080816162218.GA4512@thebird.nl>
	<20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <c27b73c0808190652i5fc9fef2l94ee31290cf545bc@mail.gmail.com>

Hi,

I've updated the Bio::PAML::Codeml::Rates class to pasrse columns with the
'*', which indicate gaps in the alignment. For instance MM*M means that
there is a gap in the alignment in the third sequence.

The changes are in my branch of bioruby.

Thanks

Mike

On Mon, Aug 18, 2008 at 7:18 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Thank you.
>
> I think PAML programs other than codeml are also valuale
> to write wrappers, especially for baseml and yn00.
>
> In BioPerl, there are four PAML program wrappers.
> (baseml, codeml, evolver, yn00)
>
> http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML
>
> So, I decide to move the codeml classes under Bio::PAML.
>
> I renamed Bio::CodeML to Bio::PAML::Codeml. Files are moved
> to bio/appl/paml/ and test/unit/bio/appl/paml/.
>
> The reason why I changed CodeML to Codeml is that
> it seems that authors of PAML do not use the word "codeML"
> (the last two letters are uppercase). Indeed, I can't find
> the word "codeML" (or "CodeML") in the PAML's documents.
>
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
>
> On Sat, 16 Aug 2008 18:22:18 +0200
> pjotr2008 at thebird.nl (Pjotr Prins) wrote:
>
> > codeml is, by far, the most valuable tool.
> >
> > Pj.
> >
> > On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> > > Hi Mike,
> > >
> > > The CodeML wrappers is now included in bioruby git.
> > > http://github.com/bioruby/bioruby/tree/master
> > >
> > > As PAML has some executables other than codeml,
> > > (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> > > I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> > > files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> > >
> > > Is it OK? (or, is codeml the only valuable component to write
> > > wrapper/parser for bioruby?)
> > >
> > > Do you (or someone) plan to write other PAML's wrappers/parsers?
> > >
> > > Thanks,
> > >
> > > Naohisa Goto
> > > ngoto at bioruby.org / ng at bioruby.org
> > >
> > >
> > > On Fri, 15 Aug 2008 20:15:09 +0900
> > > Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> > >
> > > > Hi,
> > > >
> > > > It seems good. It will be included in BioRuby.
> > > >
> > > > In my machine, a test was failed.
> > > > Can you fix the problem?
> > > (snip)
> > > >
> > > > On Wed, 13 Aug 2008 16:34:20 +0100
> > > > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > CodeML is a common tool for estimating evolutionary rate of protein
> encoding
> > > > > sequences, and is part of the PAML package. I've created a codeml
> wrapper
> > > > > and two parsers. Unit tests are also included. The code is in a
> Github fork
> > > > > in BioRuby. The fork is located here
> > > > >
> > > > > http://github.com/michaelbarton/bioruby/tree/master
> > > > >
> > > > > I like to suggested that it for inclusion in the main BioRuby
> branch.
> > > > >
> > > > > Thanks
> > > > >
> > > > > Mike
> > > > > _______________________________________________
> _______________________________________________
> 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  Tue Aug 19 14:51:18 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 19 Aug 2008 23:51:18 +0900
Subject: [BioRuby] CodeML wrapper for BioRuby
In-Reply-To: <c27b73c0808190652i5fc9fef2l94ee31290cf545bc@mail.gmail.com>
References: <c27b73c0808130834rf957166k111ed697dd6355c4@mail.gmail.com>
	<20080815111509.A4F401CBC50F@idnmail.gen-info.osaka-u.ac.jp>
	<20080816084522.5C7141CBC3F9@idnmail.gen-info.osaka-u.ac.jp>
	<20080816162218.GA4512@thebird.nl>
	<20080818061839.338471CBC4A8@idnmail.gen-info.osaka-u.ac.jp>
	<c27b73c0808190652i5fc9fef2l94ee31290cf545bc@mail.gmail.com>
Message-ID: <20080819145119.E1D101CBC541@idnmail.gen-info.osaka-u.ac.jp>

Hi,

The changes are now included in bioruby git repository.
http://github.com/bioruby/bioruby/commits/master

Thanks for improvement.

In addition, changes for Blast classes made by me
(already appeared in github.com/ngoto/bioruby) are
also included now.

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

On Tue, 19 Aug 2008 14:52:43 +0100
"Michael Barton" <mail at michaelbarton.me.uk> wrote:

> Hi,
> 
> I've updated the Bio::PAML::Codeml::Rates class to pasrse columns with the
> '*', which indicate gaps in the alignment. For instance MM*M means that
> there is a gap in the alignment in the third sequence.
> 
> The changes are in my branch of bioruby.
> 
> Thanks
> 
> Mike
> 
> On Mon, Aug 18, 2008 at 7:18 AM, Naohisa GOTO
> <ngoto at gen-info.osaka-u.ac.jp>wrote:
> 
> > Thank you.
> >
> > I think PAML programs other than codeml are also valuale
> > to write wrappers, especially for baseml and yn00.
> >
> > In BioPerl, there are four PAML program wrappers.
> > (baseml, codeml, evolver, yn00)
> >
> > http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-run/trunk/Bio/Tools/Run/Phylo/PAML
> >
> > So, I decide to move the codeml classes under Bio::PAML.
> >
> > I renamed Bio::CodeML to Bio::PAML::Codeml. Files are moved
> > to bio/appl/paml/ and test/unit/bio/appl/paml/.
> >
> > The reason why I changed CodeML to Codeml is that
> > it seems that authors of PAML do not use the word "codeML"
> > (the last two letters are uppercase). Indeed, I can't find
> > the word "codeML" (or "CodeML") in the PAML's documents.
> >
> >
> > Naohisa Goto
> > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> >
> >
> > On Sat, 16 Aug 2008 18:22:18 +0200
> > pjotr2008 at thebird.nl (Pjotr Prins) wrote:
> >
> > > codeml is, by far, the most valuable tool.
> > >
> > > Pj.
> > >
> > > On Sat, Aug 16, 2008 at 05:45:21PM +0900, Naohisa GOTO wrote:
> > > > Hi Mike,
> > > >
> > > > The CodeML wrappers is now included in bioruby git.
> > > > http://github.com/bioruby/bioruby/tree/master
> > > >
> > > > As PAML has some executables other than codeml,
> > > > (baseml, basemlg, chi2, evolver, mcmctree, pamp, yn00)
> > > > I plan to move Bio::CodeML to Bio::PAML::CodeML, and
> > > > files are moved from bio/appl/codeml to bio/appl/paml/codeml.
> > > >
> > > > Is it OK? (or, is codeml the only valuable component to write
> > > > wrapper/parser for bioruby?)
> > > >
> > > > Do you (or someone) plan to write other PAML's wrappers/parsers?
> > > >
> > > > Thanks,
> > > >
> > > > Naohisa Goto
> > > > ngoto at bioruby.org / ng at bioruby.org
> > > >
> > > >
> > > > On Fri, 15 Aug 2008 20:15:09 +0900
> > > > Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > It seems good. It will be included in BioRuby.
> > > > >
> > > > > In my machine, a test was failed.
> > > > > Can you fix the problem?
> > > > (snip)
> > > > >
> > > > > On Wed, 13 Aug 2008 16:34:20 +0100
> > > > > "Michael Barton" <mail at michaelbarton.me.uk> wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > CodeML is a common tool for estimating evolutionary rate of protein
> > encoding
> > > > > > sequences, and is part of the PAML package. I've created a codeml
> > wrapper
> > > > > > and two parsers. Unit tests are also included. The code is in a
> > Github fork
> > > > > > in BioRuby. The fork is located here
> > > > > >
> > > > > > http://github.com/michaelbarton/bioruby/tree/master
> > > > > >
> > > > > > I like to suggested that it for inclusion in the main BioRuby
> > branch.
> > > > > >
> > > > > > Thanks
> > > > > >
> > > > > > Mike
> > > > > > _______________________________________________
> > _______________________________________________
> > 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 davide.rambaldi at ifom-ieo-campus.it  Fri Aug 29 14:44:13 2008
From: davide.rambaldi at ifom-ieo-campus.it (Davide Rambaldi)
Date: Fri, 29 Aug 2008 16:44:13 +0200
Subject: [BioRuby] test and bioruby shell questions
Message-ID: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>

Greetings,
  I am a new user of ruby and bioruby and I really like it especially  
for the opportunity to test interactively with irb and BioRuby shell

  I have some question please:

- TESTING (bioruby 1.2.1 and ruby 1.8.7 on a Power PC G4 osx)
   during testing

  I got 7 errors:

  	test_gff_exportview(Bio::FuncTestEnsemblHuman) [./functional/bio/ 
io/test_ensembl.rb:95]:
	test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./ 
functional/bio/io/test_ensembl.rb:121]:
	test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./ 
functional/bio/io/test_ensembl.rb:180]:
	test_list_falsenegative(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1304]:
	test_list_falsepositive(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1356]:
	test_list_potentialhit(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1408]:
	test_list_truepositive(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1236]:

   Is a know problem or related with my computer?


- BioRuby SHELL
   during shell demo (demo command) there is a crash after:
kuma = getobj("gb:AF237819")
Retrieving entry from KEGG API (gb:AF237819)
   ==> nil
bioruby> kuma.definition
NoMethodError: undefined method `definition' for nil:NilClass
         from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in  
`irb_binding'
         from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in  
`irb_binding'
         from /usr/local/lib/ruby/1.8/irb/workspace.rb:52
Maybe IRB bug!!

   crash because kuma is empty? irb can reach the sequence?
bioruby> kuma
   ==> nil


- SHELL OBJECTS and HELP

   there is a way to delete shell objects (.bioruby/shell/session/ 
object) directly from the shell?
   a "rm" command?
   there is an help in the BioRuby shell? (help give me => nil,  ./ 
bioruby --help give unrecognized option )


Thanks and 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 donttrustben at gmail.com  Sat Aug 30 11:13:32 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Sat, 30 Aug 2008 21:13:32 +1000
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
Message-ID: <bb2b67d00808300413h4fca205bo84fad43b487a211@mail.gmail.com>

Hi,

Using the edge version of bioruby I get 7 errors as well, although
they are slightly different. I wouldn't be too worried.

$ ruby runner.rb
Loaded suite .
Started
.....FF..F.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
Finished in 133.52153 seconds.

  1) Failure:
test_gff_exportview(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:95]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  2) Failure:
test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:121]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  3) Failure:
test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:180]:
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tENSG00000206158\tENST00000382964\tENSE00001494097\tKNOWN_protein_coding\n">
expected but was
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n">.

  4) Failure:
test_id_line_sequence_version(Bio::TestEMBL)
[./unit/bio/db/embl/test_embl_rel89.rb:45]:
<"1"> expected but was
<nil>.

  5) Failure:
test_left_padding(Bio::TestStringFormatting)
[./unit/bio/util/restriction_enzyme/test_string_formatting.rb:43]:
<"nnnnnnn"> expected but was
<"">.

  6) Failure:
test_right_padding(Bio::TestStringFormatting)
[./unit/bio/util/restriction_enzyme/test_string_formatting.rb:50]:
<"nn"> expected but was
<"">.

  7) Error:
test_strip_padding(Bio::TestStringFormatting):
NoMethodError: undefined method `[]' for nil:NilClass
    ../lib/bio/util/restriction_enzyme/string_formatting.rb:64:in
`strip_padding'
    ./unit/bio/util/restriction_enzyme/test_string_formatting.rb:33:in
`test_strip_padding'

1867 tests, 4049 assertions, 6 failures, 1 errors






Can't help with the bioruby shell, sorry, as I don't use it. Why would
you want to remove objects, though?

Thanks,
ben

2008/8/30 Davide Rambaldi <davide.rambaldi at ifom-ieo-campus.it>:
> Greetings,
>  I am a new user of ruby and bioruby and I really like it especially for the
> opportunity to test interactively with irb and BioRuby shell
>
>  I have some question please:
>
> - TESTING (bioruby 1.2.1 and ruby 1.8.7 on a Power PC G4 osx)
>  during testing
>
>  I got 7 errors:
>
>        test_gff_exportview(Bio::FuncTestEnsemblHuman)
> [./functional/bio/io/test_ensembl.rb:95]:
>        test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
> [./functional/bio/io/test_ensembl.rb:121]:
>        test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
> [./functional/bio/io/test_ensembl.rb:180]:
>        test_list_falsenegative(Bio::TestPROSITE)
> [./unit/bio/db/test_prosite.rb:1304]:
>        test_list_falsepositive(Bio::TestPROSITE)
> [./unit/bio/db/test_prosite.rb:1356]:
>        test_list_potentialhit(Bio::TestPROSITE)
> [./unit/bio/db/test_prosite.rb:1408]:
>        test_list_truepositive(Bio::TestPROSITE)
> [./unit/bio/db/test_prosite.rb:1236]:
>
>  Is a know problem or related with my computer?
>
>
> - BioRuby SHELL
>  during shell demo (demo command) there is a crash after:
> kuma = getobj("gb:AF237819")
> Retrieving entry from KEGG API (gb:AF237819)
>  ==> nil
> bioruby> kuma.definition
> NoMethodError: undefined method `definition' for nil:NilClass
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in `irb_binding'
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in `irb_binding'
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52
> Maybe IRB bug!!
>
>  crash because kuma is empty? irb can reach the sequence?
> bioruby> kuma
>  ==> nil
>
>
> - SHELL OBJECTS and HELP
>
>  there is a way to delete shell objects (.bioruby/shell/session/object)
> directly from the shell?
>  a "rm" command?
>  there is an help in the BioRuby shell? (help give me => nil,  ./bioruby
> --help give unrecognized option )
>
>
> Thanks and 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)
>
> -----------------------------------------------------
>
>
>
>
> _______________________________________________
> 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 ktym at hgc.jp  Sat Aug 30 12:16:01 2008
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Sat, 30 Aug 2008 21:16:01 +0900
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
Message-ID: <992DF6FE-14DF-45B9-B141-224FF473E82B@hgc.jp>

Dear Davide,

On 2008/08/29, at 23:44, Davide Rambaldi wrote:
> - BioRuby SHELL
>  during shell demo (demo command) there is a crash after:
> kuma = getobj("gb:AF237819")
> Retrieving entry from KEGG API (gb:AF237819)
>  ==> nil
> bioruby> kuma.definition
> NoMethodError: undefined method `definition' for nil:NilClass
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in `irb_binding'
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in `irb_binding'
>        from /usr/local/lib/ruby/1.8/irb/workspace.rb:52
> Maybe IRB bug!!
>
>  crash because kuma is empty? irb can reach the sequence?
> bioruby> kuma
>  ==> nil

This feature (obtaining GenBank entry by getobj method) is temporally unavailable
because of the discontinuation of the GenBank retrieval service in KEGG API
developed at the Kyoto University in Japan.

The demo above was designed to utilize the KEGG API, which is a SOAP based web service,
so we need to change the default data source to obtain this entry.
We can fix this by switching to use NCBI's efetch method instead.


> - SHELL OBJECTS and HELP
>
>  there is a way to delete shell objects (.bioruby/shell/session/object) directly from the shell?
>  a "rm" command?

Yes.

If you have a large object which you don't want to save persistently over the sessions,

bioruby> a = "atgc" * 10000

you can remove it by the name of the variable

bioruby> rm "a"

or by the symbol of the variable name

bioruby> rm :a

Actually, the rm command temporally assign 'nil' to the variable
because BioRuby shell will avoid to dump variables having 'nil' as its value.
(This means, the memory will not be returned to the OS until next GC.)

This implementation looks somewhat ugly, so if you have a better idea, please let me know.


>  there is an help in the BioRuby shell? (help give me => nil,  ./bioruby --help give unrecognized option )

Planned but never implemented. Sorry.

Regards,
Toshiaki Katayama





From ngoto at gen-info.osaka-u.ac.jp  Sun Aug 31 04:05:52 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sun, 31 Aug 2008 13:05:52 +0900
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
Message-ID: <20080831040553.5381A1CBC3AF@idnmail.gen-info.osaka-u.ac.jp>

Hi,

Thank you for reporting.

On Fri, 29 Aug 2008 16:44:13 +0200
Davide Rambaldi <davide.rambaldi at ifom-ieo-campus.it> wrote:

> Greetings,
>   I am a new user of ruby and bioruby and I really like it especially  
> for the opportunity to test interactively with irb and BioRuby shell
> 
>   I have some question please:
> 
> - TESTING (bioruby 1.2.1 and ruby 1.8.7 on a Power PC G4 osx)
>    during testing
> 
>   I got 7 errors:
> 
>   	test_gff_exportview(Bio::FuncTestEnsemblHuman) [./functional/bio/ 
> io/test_ensembl.rb:95]:
> 	test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./ 
> functional/bio/io/test_ensembl.rb:121]:
> 	test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./ 
> functional/bio/io/test_ensembl.rb:180]:

Next time, please show all failure message, even if long.

Perhaps they are caused by the change of the Ensembl.
For a reminder, I submitted to the bug tracking system of BioRuby.
http://rubyforge.org/tracker/index.php?func=detail&aid=21744&group_id=769&atid=3037

> 	test_list_falsenegative(Bio::TestPROSITE) [./unit/bio/db/ 
> test_prosite.rb:1304]:
> 	test_list_falsepositive(Bio::TestPROSITE) [./unit/bio/db/ 
> test_prosite.rb:1356]:
> 	test_list_potentialhit(Bio::TestPROSITE) [./unit/bio/db/ 
> test_prosite.rb:1408]:
> 	test_list_truepositive(Bio::TestPROSITE) [./unit/bio/db/ 
> test_prosite.rb:1236]:

These are caused by changes of order of data in arrays, due to
the change of hash algorithm in Ruby 1.8.7 (and in Ruby 1.9.0).

I fixed these tests not to affected by order of data.
This is already included in git repository.
http://github.com/bioruby/bioruby/commit/e86f8d757c45805389e154f06ccde5a3d9e8a557

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


From ngoto at gen-info.osaka-u.ac.jp  Sun Aug 31 04:25:46 2008
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sun, 31 Aug 2008 13:25:46 +0900
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <bb2b67d00808300413h4fca205bo84fad43b487a211@mail.gmail.com>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<bb2b67d00808300413h4fca205bo84fad43b487a211@mail.gmail.com>
Message-ID: <20080831042546.D246F1CBC56E@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Sat, 30 Aug 2008 21:13:32 +1000
"Ben Woodcroft" <donttrustben at gmail.com> wrote:

> Hi,
> 
> Using the edge version of bioruby I get 7 errors as well, although
> they are slightly different. I wouldn't be too worried.

What BioRuby version, Ruby version, and OS and CPU did you use?

> 
> $ ruby runner.rb
> Loaded suite .
> Started
> .....FF..F..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
 .!
>  ..............................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
> Finished in 133.52153 seconds.
> 
  1) Failure:
test_gff_exportview(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:95]:
(snip)

1) to 3) seems the same as the previous mail.
http://rubyforge.org/tracker/index.php?func=detail&aid=21744&group_id=769&atid=3037
This still remains unfixed.

>   4) Failure:
> test_id_line_sequence_version(Bio::TestEMBL)
> [./unit/bio/db/embl/test_embl_rel89.rb:45]:
> <"1"> expected but was
> <nil>.

I see this first time.
Which bioruby version?

>   5) Failure:
> test_left_padding(Bio::TestStringFormatting)
> [./unit/bio/util/restriction_enzyme/test_string_formatting.rb:43]:
> <"nnnnnnn"> expected but was
> <"">.
> 
>   6) Failure:
> test_right_padding(Bio::TestStringFormatting)
> [./unit/bio/util/restriction_enzyme/test_string_formatting.rb:50]:
> <"nn"> expected but was
> <"">.
> 
>   7) Error:
> test_strip_padding(Bio::TestStringFormatting):
> NoMethodError: undefined method `[]' for nil:NilClass
>     ../lib/bio/util/restriction_enzyme/string_formatting.rb:64:in
> `strip_padding'
>     ./unit/bio/util/restriction_enzyme/test_string_formatting.rb:33:in
> `test_strip_padding'
> 
> 1867 tests, 4049 assertions, 6 failures, 1 errors
> 

I believe commit 735e3563b723645afa65f0e4213a7c92152f68ec
fixed 5) to 7).

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


From donttrustben at gmail.com  Sun Aug 31 07:11:31 2008
From: donttrustben at gmail.com (Ben Woodcroft)
Date: Sun, 31 Aug 2008 17:11:31 +1000
Subject: [BioRuby] test and bioruby shell questions
In-Reply-To: <20080831042546.D246F1CBC56E@idnmail.gen-info.osaka-u.ac.jp>
References: <3AF7B27B-E642-48FD-A612-ED88E9FF28BC@ifom-ieo-campus.it>
	<bb2b67d00808300413h4fca205bo84fad43b487a211@mail.gmail.com>
	<20080831042546.D246F1CBC56E@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <bb2b67d00808310011p7232608dk645434272f729e4b@mail.gmail.com>

Hi,

Thanks for your concern.
After pulling from the newest github -
http://github.com/bioruby/bioruby/commit/e86f8d757c45805389e154f06ccde5a3d9e8a557

$ ruby -v
ruby 1.8.6 (2007-09-24 patchlevel 111) [i486-linux]
$ uname -a
Linux uyen 2.6.24-21-generic #1 SMP Mon Aug 25 17:32:09 UTC 2008 i686 GNU/Linux

Using Ubuntu Hardy, and the latest patched version of the ruby1.8
package (1.8.6.111-2ubuntu1.1)

$ ruby runner.rb
Loaded suite .
Started
.....FF..F.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
Finished in 142.816902 seconds.

  1) Failure:
test_gff_exportview(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:95]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  2) Failure:
test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:121]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  3) Failure:
test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:180]:
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tENSG00000206158\tENST00000382964\tENSE00001494097\tKNOWN_protein_coding\n">
expected but was
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n">.

  4) Failure:
test_id_line_sequence_version(Bio::TestEMBL)
[./unit/bio/db/embl/test_embl_rel89.rb:45]:
<"1"> expected but was
<nil>.

  5) Failure:
test_left_padding(Bio::TestStringFormatting)
[./unit/bio/util/restriction_enzyme/test_string_formatting.rb:43]:
<"nnnnnnn"> expected but was
<"">.

  6) Failure:
test_right_padding(Bio::TestStringFormatting)
[./unit/bio/util/restriction_enzyme/test_string_formatting.rb:50]:
<"nn"> expected but was
<"">.

  7) Error:
test_strip_padding(Bio::TestStringFormatting):
NoMethodError: undefined method `[]' for nil:NilClass
    ../lib/bio/util/restriction_enzyme/string_formatting.rb:64:in
`strip_padding'
    ./unit/bio/util/restriction_enzyme/test_string_formatting.rb:33:in
`test_strip_padding'

1867 tests, 4049 assertions, 6 failures, 1 errors

I don't actually care personally about these problems, but am glad to
help out in a general sense.

Thanks,
ben



2008/8/31 Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp>:
> Hi,
>
> On Sat, 30 Aug 2008 21:13:32 +1000
> "Ben Woodcroft" <donttrustben at gmail.com> wrote:
>
>> Hi,
>>
>> Using the edge version of bioruby I get 7 errors as well, although
>> they are slightly different. I wouldn't be too worried.
>
> What BioRuby version, Ruby version, and OS and CPU did you use?
>
>>
>> $ ruby runner.rb
>> Loaded suite .
>> Started
>> .....FF..F..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
>  .!
>>  ..............................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
>> Finished in 133.52153 seconds.
>>
>  1) Failure:
> test_gff_exportview(Bio::FuncTestEnsemblHuman)
> [./functional/bio/io/test_ensembl.rb:95]:
> (snip)
>
> 1) to 3) seems the same as the previous mail.
> http://rubyforge.org/tracker/index.php?func=detail&aid=21744&group_id=769&atid=3037
> This still remains unfixed.
>
>>   4) Failure:
>> test_id_line_sequence_version(Bio::TestEMBL)
>> [./unit/bio/db/embl/test_embl_rel89.rb:45]:
>> <"1"> expected but was
>> <nil>.
>
> I see this first time.
> Which bioruby version?
>
>>   5) Failure:
>> test_left_padding(Bio::TestStringFormatting)
>> [./unit/bio/util/restriction_enzyme/test_string_formatting.rb:43]:
>> <"nnnnnnn"> expected but was
>> <"">.
>>
>>   6) Failure:
>> test_right_padding(Bio::TestStringFormatting)
>> [./unit/bio/util/restriction_enzyme/test_string_formatting.rb:50]:
>> <"nn"> expected but was
>> <"">.
>>
>>   7) Error:
>> test_strip_padding(Bio::TestStringFormatting):
>> NoMethodError: undefined method `[]' for nil:NilClass
>>     ../lib/bio/util/restriction_enzyme/string_formatting.rb:64:in
>> `strip_padding'
>>     ./unit/bio/util/restriction_enzyme/test_string_formatting.rb:33:in
>> `test_strip_padding'
>>
>> 1867 tests, 4049 assertions, 6 failures, 1 errors
>>
>
> I believe commit 735e3563b723645afa65f0e4213a7c92152f68ec
> fixed 5) to 7).
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> _______________________________________________
> 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.