From ngoto at gen-info.osaka-u.ac.jp  Wed May  6 03:56:48 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Wed, 6 May 2009 16:56:48 +0900
Subject: [BioRuby] Made a change in format10.rb
In-Reply-To: <49B4B4EA.6060401@bioreg.kyushu-u.ac.jp>
References: <49B4B4EA.6060401@bioreg.kyushu-u.ac.jp>
Message-ID: <20090506075650.37E4A1CBC4EB@idnmail.gen-info.osaka-u.ac.jp>

Hi,

Thank you for reporting a bug.

I've changed codes to support results containing two or
more query sequences.

http://github.com/bioruby/bioruby/commit/e57349594427ad1a51979c9d4e0c3efcffd160c2
http://github.com/bioruby/bioruby/commit/3d3edc44127f4fd97abcc17a859e36623facdc7c


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


On Mon, 09 Mar 2009 15:19:22 +0900
Fredrik Johansson <fredjoha at bioreg.kyushu-u.ac.jp> wrote:

> I found that Bioruby can't handle large amounts of output from Fasta. So 
> I made this change to 
> /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/fasta/format10.rb :
> 
> 6,7c6,8
> <       data.sub!(/(.*)\n\n>>>/m, '')
> <       @list = "The best scores are" + $1
> ---
>  >       border = data.index("\n\n>>>")
>  >       @list = "The best scores are" + data[0...border]
>  >       data = data[border+5..-1]
> 
> 
> The old code reported an error when the output was huge:
> RegexpError: Stack overflow in regexp matcher: /(.*)\n\n>>>/m
> 
> So I thought that maybe these lines of code should be changed in Bioruby.
> 
> Regards,
> Fredrik Johansson
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

From andrew.j.grimm at gmail.com  Thu May  7 03:31:26 2009
From: andrew.j.grimm at gmail.com (Andrew Grimm)
Date: Thu, 7 May 2009 17:31:26 +1000
Subject: [BioRuby] Non deprecated way of converting a naseq to fasta?
Message-ID: <b9140daa0905070031y6effb190sc4084e08f5fd0ac0@mail.gmail.com>

The documentation for Bio::Sequence::Common talks about #to_fasta being
deprecated, in favor of Bio::Sequence #output instead. #output seems to work
for Bio::Sequence objects, but not for Bio::Sequence::NA or
Bio::Sequence::AA objects.

I can happily create a new FastaFormat object instead, but I'm wondering if
I'm doing it the right way.

Also, the wiki is still suggesting using to_fasta in some of its code
samples.

Thanks,

Andrew Grimm

From ngoto at gen-info.osaka-u.ac.jp  Wed May 13 10:55:12 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Wed, 13 May 2009 23:55:12 +0900
Subject: [BioRuby] Non deprecated way of converting a naseq to fasta?
In-Reply-To: <b9140daa0905070031y6effb190sc4084e08f5fd0ac0@mail.gmail.com>
References: <b9140daa0905070031y6effb190sc4084e08f5fd0ac0@mail.gmail.com>
Message-ID: <20090513145512.D17251CBC3CB@idnmail.gen-info.osaka-u.ac.jp>

On Thu, 7 May 2009 17:31:26 +1000
Andrew Grimm <andrew.j.grimm at gmail.com> wrote:

> The documentation for Bio::Sequence::Common talks about #to_fasta being
> deprecated, in favor of Bio::Sequence #output instead. #output seems to work
> for Bio::Sequence objects, but not for Bio::Sequence::NA or
> Bio::Sequence::AA objects.

Because the method "to_fasta" is widely and frequently used,
and alternative methods are not fully implemented, you can
still use "to_fasta".

Why "to_fasta" is planned to be deprecated is that the name
to_XXX is usually used for data class conversion in Ruby but
the current behavior of "to_fasta" is to output formatted string.

The method "to_fasta" will be deprecated in the future release,
after alternative methods are fully ready. In addition, for
smooth migration, "to_fasta" may exist as an alias (or a shortcut)
of the alternative methods for a while.

> I can happily create a new FastaFormat object instead, but I'm wondering if
> I'm doing it the right way.

To create a new Bio::Sequence object is the best way.
Bio::FastaFormat is a parser class for reading formatted string,
and is not be intended to generate formatted string.

> Also, the wiki is still suggesting using to_fasta in some of its code
> samples.

Those will be rewritten in the future.

> 
> Thanks,
> 
> Andrew Grimm
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

Thank you.

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

From pjotr.public14 at thebird.nl  Sat May 16 03:57:34 2009
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sat, 16 May 2009 09:57:34 +0200
Subject: [BioRuby] Google Summer of Code Intro: PhyloXML support
	in	BioRuby
In-Reply-To: <4057d3bf0904301837r302bfb2buaa8a644c448267fa@mail.gmail.com>
References: <4057d3bf0904301837r302bfb2buaa8a644c448267fa@mail.gmail.com>
Message-ID: <20090516075734.GA27669@thebird.nl>

Hi Diana,

I think your contribution will be very important for BioRuby, and as
you are implementing together with others who are adding support for
BioPerl and BioPython I have great faith in you getting results.

Thank you for taking an interest. We are looking forward to your
contribution. If you have any questions on BioRuby ideas and options,
please post to this list. Note that responses can be slow, but
everyone is tracking.

Pj.

On Thu, Apr 30, 2009 at 09:37:07PM -0400, Diana Jaunzeikare wrote:
> Hi all,
> 
> I would like to introduce myself. My name is Diana and I have been accepted
> for Google Summer of Code to implement PhyloXML support for BioRuby. I am a
> junior at Smith College double majoring in Computer Science and Math. I am
> interested in Bioinformatics, especially protein structure based
> phylogenetics.
> 
> Here is the project abstract:
> 
> ===
> Phylogenetic trees are used in important applications, including
> phylogenomics, phylogeography, gene function prediction, cladistics and the
> study of molecular evolution. In order to foster successful analysis,
> exchange, storage and reuse of phylogenetic trees and associated data, the
> phyloXML format was developed. It can store all necessary information about
> the phylogenetic tree, like clade, sequence, name and distance. The goal of
> this project is to implement support for phyloXML in BioRuby.
> ===
> 
> Here is wiki:
> https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
> 
> 
> Any comments are welcome!
> 
> Cheers,
> 
> Diana
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

From georgkam at gmail.com  Sat May 16 08:20:59 2009
From: georgkam at gmail.com (George Githinji)
Date: Sat, 16 May 2009 15:20:59 +0300
Subject: [BioRuby] Fwd: [BioSQL-l] BioSQL at BOSC 2009?
In-Reply-To: <320fb6e00905160512m66848611l432a81f22866b37f@mail.gmail.com>
References: <320fb6e00905160512m66848611l432a81f22866b37f@mail.gmail.com>
Message-ID: <55915f820905160520p1204f35bpbc63b6cabd936c53@mail.gmail.com>

---------- Forwarded message ----------
From: Peter <biopython at maubp.freeserve.co.uk>
Date: Sat, May 16, 2009 at 3:12 PM
Subject: [BioSQL-l] BioSQL at BOSC 2009?
To: biosql-l <biosql-l at lists.open-bio.org>
Cc: Jason Stajich <jason at bioperl.org>


Hi,

Will any of the key BioSQL people from the Bio* projects be at BOSC
(and ISMB) this year? http://open-bio.org/wiki/BOSC_2009

There will be several people from Biopython there this year, including
me and Brad Chapman who are both familiar with BioSQL.  This would be
a nice opportunity for further improving BioSQL compatibility between
the Bio* projects - something that has been suggested in the past,
e.g.

http://lists.open-bio.org/pipermail/biopython/2007-November/003893.html
http://lists.open-bio.org/pipermail/biojava-l/2007-November/006037.html

I don't follow the BioPerl, BioJava or BioRuby mailing lists - and I
doubt many of their developers follow the Biopython mailing lists.
So, rather than having any BioSQL compatibility discussions split over
individual Bio* project specific mailing lists, it seems using the
BioSQL mailing list is most appropriate.

I have CC'd a few key people just in case they are not on the BioSQL
mailing list, if I have missed anyone please forward this to them and
ask them to sign up.

Thanks,

Peter
_______________________________________________
BioSQL-l mailing list
BioSQL-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biosql-l



-- 
---------------
Sincerely
George

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

From bonnalraoul at ingm.it  Mon May 18 04:13:47 2009
From: bonnalraoul at ingm.it (Raoul JP Bonnal)
Date: Mon, 18 May 2009 10:13:47 +0200
Subject: [BioRuby] Meet Italian Developers
Message-ID: <4A1118BB.6070205@ingm.it>

Hi Guys,
I'd like to meet Italians' BioRuby developers.
Do you think would be possible to organize an informal meeting in Milan ?
Then I'd like to know how many BioRuby devs are following the list.

--
Ra


From rozziite at gmail.com  Tue May 19 17:07:59 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Tue, 19 May 2009 17:07:59 -0400
Subject: [BioRuby] Update on phyloXML support for BioRuby project
Message-ID: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>

Hi all,

I want to update you on my thoughts about this project and I have some
questions.

So, I think we have reached consensus that the best choice is libxml2-ruby
SAX based XML parser.

Since BioRuby has Tree class ( http://bioruby.org/rdoc/) it seems logical
that the parser should return a Tree class object. By using SAX parser we
avoid the problem of having whole XML file in memory, but still the
phylogenetic trees can be very large, and it might be too much to store
whole thing as a tree object in memory. This could be a little remediated by
having a function next_tree (or next_phylogeny) which would read one tree at
a time if phyloXML file has several of them (this is similar to BioPerl
implementation). I don't think the children nodes can be done in similar
fashion. Since SAX parses sequentially, to get next node (child one level
down) in the tree, whole subtree has to be parsed (in order to wait while
there is event for the end tag of that child), thus loosing on speed. Any
thoughts on this?

Also the Tree class should be extended and added method output_phyloXML
since it has methods output_newick, output_nhx.

I think in order to understand what should be returned after parsing it
would be useful to know how people use phylogenetic tree data. Here are some
I could come up,
* visualize / print
* calculate total branch length of a tree
* query info about specific nodes
* create consensus trees
Any others?

I am a little confused about the require statements in BioRuby classes. It
looks like bio/tree.rb should hold a general class, but it requires
bio/db/newick.rb, but this file in turn requires bio/tree.rb.

Thanks,

Diana

Project Page:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby

From czmasek at burnham.org  Tue May 19 17:54:18 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Tue, 19 May 2009 14:54:18 -0700
Subject: [BioRuby] Update on phyloXML support for BioRuby project
In-Reply-To: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
Message-ID: <4A132A8A.70102@burnham.org>

Hi, Diana:

I think it is a good idea to have the parser return one tree at a time, 
as opposed to returning a list of trees.

On the other hand, the same does not apply to nodes. I think it is 
perfectly acceptable to expect to have enough memory to keep at least 
one tree in memory (a good target size might be a binary tree with 
ten-thousand external nodes and 200 bytes of annotation per node, which 
according to my rough calculations would require less than 5MB).

For your tree use cases, important ones to add are:
* iteration over all nodes
* retrieval/finding of specific nodes according to some criterion (e.g. 
find all nodes for which the species is "E. coli")
* tree reconciliation (e.g. compare a gene tree to a species tree, in 
order to determine duplications on the gene tree)

In any case, all these applications/algorithms will be most time 
efficient and easiest to implement with trees which are completely in 
memory.

Re. "I am a little confused about the require statements in BioRuby 
classes. It looks like bio/tree.rb should hold a general class, but it 
requires bio/db/newick.rb, but this file in turn requires bio/tree.rb."

I am not clear about your question about this. ;)

Christian


Diana Jaunzeikare wrote:
> Hi all,
>
> I want to update you on my thoughts about this project and I have some 
> questions.
>
> So, I think we have reached consensus that the best choice is 
> libxml2-ruby SAX based XML parser.
>
> Since BioRuby has Tree class ( http://bioruby.org/rdoc/) it seems 
> logical that the parser should return a Tree class object. By using 
> SAX parser we avoid the problem of having whole XML file in memory, 
> but still the phylogenetic trees can be very large, and it might be 
> too much to store whole thing as a tree object in memory. This could 
> be a little remediated by having a function next_tree (or 
> next_phylogeny) which would read one tree at a time if phyloXML file 
> has several of them (this is similar to BioPerl implementation). I 
> don't think the children nodes can be done in similar fashion. Since 
> SAX parses sequentially, to get next node (child one level down) in 
> the tree, whole subtree has to be parsed (in order to wait while there 
> is event for the end tag of that child), thus loosing on speed. Any 
> thoughts on this?
>
> Also the Tree class should be extended and added method 
> output_phyloXML since it has methods output_newick, output_nhx.
>
> I think in order to understand what should be returned after parsing 
> it would be useful to know how people use phylogenetic tree data. Here 
> are some I could come up,
> * visualize / print
> * calculate total branch length of a tree
> * query info about specific nodes
> * create consensus trees
> Any others?
>
> I am a little confused about the require statements in BioRuby 
> classes. It looks like bio/tree.rb should hold a general class, but it 
> requires bio/db/newick.rb, but this file in turn requires bio/tree.rb.
>
> Thanks,
>
> Diana
>
> Project Page: 
> https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
>


From ngoto at gen-info.osaka-u.ac.jp  Wed May 20 02:09:17 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Wed, 20 May 2009 15:09:17 +0900
Subject: [BioRuby] Update on phyloXML support for BioRuby project
In-Reply-To: <4A132A8A.70102@burnham.org>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
Message-ID: <20090520060918.B07C71CBC3F4@idnmail.gen-info.osaka-u.ac.jp>

Hi all,

On Tue, 19 May 2009 17:07:59 -0400
Diana Jaunzeikare <rozziite at gmail.com> wrote:

> So, I think we have reached consensus that the best choice is libxml2-ruby
> SAX based XML parser.

In libxml2-ruby, I think LibXML::XML::Reader is the best choice,
because it is memory efficient than DOM and its API is simpler
than that of SAX. LibXML::XML::SAXParser is not bad, but I wonder
if the SAX's callback based API makes our codes too complex and
difficult to maintain.

> Since BioRuby has Tree class ( http://bioruby.org/rdoc/) it seems 
> logical that the parser should return a Tree class object. By using 
> SAX parser we avoid the problem of having whole XML file in memory, 

I think so.
Alternative way is to return an object of wrapper class which mimics
Bio::Tree's API. However, it may be too hard to implement such class,
and data type conversion from/to Bio::Tree is still needed even in
this case. So, I think to return a Bio::Tree object is good.

> I am a little confused about the require statements in BioRuby classes. It
> looks like bio/tree.rb should hold a general class, but it requires
> bio/db/newick.rb, but this file in turn requires bio/tree.rb.

The only reason why bio/tree.rb requires bio/db/newick.rb is
for the Newick and NHX output of the tree.  The codes will
be refactored in the future.

On Tue, 19 May 2009 14:54:18 -0700
Christian M Zmasek <czmasek at burnham.org> wrote:

> Hi, Diana:
> 
> I think it is a good idea to have the parser return one tree at a time, 
> as opposed to returning a list of trees.

I think so.

> On the other hand, the same does not apply to nodes. I think it is 
> perfectly acceptable to expect to have enough memory to keep at least 
> one tree in memory (a good target size might be a binary tree with 
> ten-thousand external nodes and 200 bytes of annotation per node, which 
> according to my rough calculations would require less than 5MB).
> 
> For your tree use cases, important ones to add are:
> * iteration over all nodes
> * retrieval/finding of specific nodes according to some criterion (e.g. 
> find all nodes for which the species is "E. coli")
> * tree reconciliation (e.g. compare a gene tree to a species tree, in 
> order to determine duplications on the gene tree)
> 
> In any case, all these applications/algorithms will be most time 
> efficient and easiest to implement with trees which are completely in 
> memory.

In addition, it is easy to implement manipulation of trees
(adding/deleting nodes and edges, etc.).

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


From rozziite at gmail.com  Wed May 20 10:51:26 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Wed, 20 May 2009 10:51:26 -0400
Subject: [BioRuby] Update on phyloXML support for BioRuby project
In-Reply-To: <20090520060918.B07C71CBC3F4@idnmail.gen-info.osaka-u.ac.jp>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<4A132A8A.70102@burnham.org>
	<20090520060918.B07C71CBC3F4@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <4057d3bf0905200751u739b37cdqe1e7d275fb82d08c@mail.gmail.com>

On Wed, May 20, 2009 at 2:09 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi all,
>
> On Tue, 19 May 2009 17:07:59 -0400
> Diana Jaunzeikare <rozziite at gmail.com> wrote:
>
> > So, I think we have reached consensus that the best choice is
> libxml2-ruby
> > SAX based XML parser.
>
> In libxml2-ruby, I think LibXML::XML::Reader is the best choice,
> because it is memory efficient than DOM and its API is simpler
> than that of SAX. LibXML::XML::SAXParser is not bad, but I wonder
> if the SAX's callback based API makes our codes too complex and
> difficult to maintain.
>

I wrote sample code using both LibXML::XML::Reader and
LibXML::XML::SAXParser and I agree that SAX's callback based API might get
very complex and hard to maintain.


>
> > Since BioRuby has Tree class ( http://bioruby.org/rdoc/) it seems
> > logical that the parser should return a Tree class object. By using
> > SAX parser we avoid the problem of having whole XML file in memory,
>
> I think so.
> Alternative way is to return an object of wrapper class which mimics
> Bio::Tree's API. However, it may be too hard to implement such class,
> and data type conversion from/to Bio::Tree is still needed even in
> this case. So, I think to return a Bio::Tree object is good.
>
> > I am a little confused about the require statements in BioRuby classes.
> It
> > looks like bio/tree.rb should hold a general class, but it requires
> > bio/db/newick.rb, but this file in turn requires bio/tree.rb.
>
> The only reason why bio/tree.rb requires bio/db/newick.rb is
> for the Newick and NHX output of the tree.  The codes will
> be refactored in the future.
>
> On Tue, 19 May 2009 14:54:18 -0700
> Christian M Zmasek <czmasek at burnham.org> wrote:
>
> > Hi, Diana:
> >
> > I think it is a good idea to have the parser return one tree at a time,
> > as opposed to returning a list of trees.
>
> I think so.
>
> > On the other hand, the same does not apply to nodes. I think it is
> > perfectly acceptable to expect to have enough memory to keep at least
> > one tree in memory (a good target size might be a binary tree with
> > ten-thousand external nodes and 200 bytes of annotation per node, which
> > according to my rough calculations would require less than 5MB).
> >
> > For your tree use cases, important ones to add are:
> > * iteration over all nodes
> > * retrieval/finding of specific nodes according to some criterion (e.g.
> > find all nodes for which the species is "E. coli")
> > * tree reconciliation (e.g. compare a gene tree to a species tree, in
> > order to determine duplications on the gene tree)
> >
> > In any case, all these applications/algorithms will be most time
> > efficient and easiest to implement with trees which are completely in
> > memory.
>
> In addition, it is easy to implement manipulation of trees
> (adding/deleting nodes and edges, etc.).
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
>

From rozziite at gmail.com  Wed May 20 22:29:40 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Wed, 20 May 2009 22:29:40 -0400
Subject: [BioRuby] [Wg-phyloinformatics] Update on phyloXML support for
	BioRubyproject
In-Reply-To: <1E5916D0F3C84F978A4A62DD89275053@NewLife>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu> 
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<1E5916D0F3C84F978A4A62DD89275053@NewLife>
Message-ID: <4057d3bf0905201929y658cb924r36c2d48f62176ed4@mail.gmail.com>

Both nexml and phyloxml are xml formats for holding information about
phylogenetic trees. Both seem to be fairly new. What's the difference? Isn't
there an ultimate goal to have one universal format for phylogenetic data
exchnage? If yes, which of these two formats would be better suitable for
it, or do they serve different purposes (as nexml is based on NEXUS format)?



My other question is about Perl phylogenetics related packages (warning: Iam
not familiar at all with BioPerl classes). Bio::TreeIO and Bio::Phylo::IO
for me seem to be doing the same task. What are the main differences between
them? If there are no fundamental differences, why there are two classes
which do the same thing.

Diana


On Wed, May 20, 2009 at 11:13 AM, Mark A. Jensen <maj at fortinbras.us> wrote:

> Should I plug my "web service blog":
>
> https://www.nescent.org/wg_evoinfo/User_talk:Mjensen#.22Streaming.22_NeXML.3F?
> Some possible useful ideas there. I've also written a flexible DOM
> implementation for Bio::Phylo, that could be
> generalized/cannibalized/stolen and
> used for iterating/streaming XML formats. It provides a standard interface
> for
> writing dom elements, but allows for easily swapping in different XML
> handling
> packages (in a BioPerly '-format => libxml' way). All in Perl I'm afraid
> (or
> proud?) to say, but it might provide ideas too. (I sent it to Rutger, but
> he
> hasn't passed judgment yet, so it's currently available 'by request to the
> author'.)
> cheers; excellent work Diana- MAJ
>
> ----- Original Message -----
> From: "Chris Fields" <cjfields at illinois.edu>
> To: "Hilmar Lapp" <hlapp at duke.edu>
> Cc: <bioruby at lists.open-bio.org>; "Phyloinformatics Group"
> <Wg-phyloinformatics at nescent.org>
> Sent: Wednesday, May 20, 2009 10:52 AM
> Subject: Re: [Wg-phyloinformatics] Update on phyloXML support for
> BioRubyproject
>
>
> >
> > On May 20, 2009, at 8:22 AM, Hilmar Lapp wrote:
> >
> >>
> >> On May 19, 2009, at 5:54 PM, Christian M Zmasek wrote:
> >>
> >>> I think it is perfectly acceptable to expect to have enough memory
> >>> to keep at least
> >>> one tree in memory
> >>
> >> Sounds like a good and perfectly reasonable starting point to me too.
> >> It's also the way other toolkits (such as BioPerl) work.
> >>
> >> Having said that, I don't find it inconceivable that we may be working
> >> with trees in the near future that don't fit into memory for a 1GB RAM
> >> machine if they are richly decorated (which is something that phyloXML
> >> wants to enable, isn't it?). Solving that to me though seems to be
> >> question of writing an appropriate Tree implementation that happens to
> >> store most of the data on disk rather than in memory, and not an issue
> >> for how to write a parser. Ideally though, the parser uses a factory
> >> for creating the (tree and/or node) objects, so that later it can be
> >> made to use an on-disk Tree implementation simply by passing it
> >> another factory. I.e., ideally the parser would not assume and hard-
> >> code the Tree implementation class.
> >>
> >> Just my $0.02.
> >>
> >> -hilmar
> >
> > This could be implemented in a lazy way or using lightweight objects.
> > The Tree object itself contains the XML parser or a reference thereof
> > (probably LibXML Reader-based) and creates the relevant nodes as
> > needed.  The only thing needed would be some light parsing to indicate
> > start-end file points.
> >
> > It's tricky with re: to a number of aspects, but it can be done.  For
> > instance, if one wanted to modify the created nodes (i.e. if the nodes
> > are mutable), or creating a generic Lazy set of classes capable of
> > dealing with multiple formats.
> >
> > Just in case anyone's wondering, I have been thinking along these
> > lines for a while re: BioPerl, Bio::Seq, and very large files... ;>
> >
> > chris
> > _______________________________________________
> > Wg-phyloinformatics mailing list
> > Wg-phyloinformatics at nescent.org
> > https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
> >
> >
>
> _______________________________________________
> Wg-phyloinformatics mailing list
> Wg-phyloinformatics at nescent.org
> https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
>

From czmasek at burnham.org  Thu May 21 00:02:11 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Wed, 20 May 2009 21:02:11 -0700
Subject: [BioRuby] [Wg-phyloinformatics] Update on phyloXML support for
 BioRuby project
In-Reply-To: <D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
Message-ID: <4A14D243.2010101@burnham.org>

Hi:

Thanks for the detailed replies by Hilmar and Chris!
I think it is a very good idea to keep such very large trees in mind, 
and possibly implement a solution which only loads requested nodes into 
memory (as described by Hilmar and Chris) if there is enough time left 
at the end of the project.

Re "It's tricky with re: to a number of aspects, but it can be done.  For  
instance, if one wanted to modify the created nodes (i.e. if the nodes  
are mutable), or creating a generic Lazy set of classes capable of   
dealing with multiple formats."

How would you do post-order or pre-order iteration of nodes? Wouldn't you have to back and forth in the file?

CZ

Chris Fields wrote:
> On May 20, 2009, at 8:22 AM, Hilmar Lapp wrote:
>
>   
>> On May 19, 2009, at 5:54 PM, Christian M Zmasek wrote:
>>
>>     
>>> I think it is perfectly acceptable to expect to have enough memory
>>> to keep at least
>>> one tree in memory
>>>       
>> Sounds like a good and perfectly reasonable starting point to me too.
>> It's also the way other toolkits (such as BioPerl) work.
>>
>> Having said that, I don't find it inconceivable that we may be working
>> with trees in the near future that don't fit into memory for a 1GB RAM
>> machine if they are richly decorated (which is something that phyloXML
>> wants to enable, isn't it?). Solving that to me though seems to be
>> question of writing an appropriate Tree implementation that happens to
>> store most of the data on disk rather than in memory, and not an issue
>> for how to write a parser. Ideally though, the parser uses a factory
>> for creating the (tree and/or node) objects, so that later it can be
>> made to use an on-disk Tree implementation simply by passing it
>> another factory. I.e., ideally the parser would not assume and hard-
>> code the Tree implementation class.
>>
>> Just my $0.02.
>>
>> 	-hilmar
>>     
>
> This could be implemented in a lazy way or using lightweight objects.   
> The Tree object itself contains the XML parser or a reference thereof  
> (probably LibXML Reader-based) and creates the relevant nodes as  
> needed.  The only thing needed would be some light parsing to indicate  
> start-end file points.
>
> It's tricky with re: to a number of aspects, but it can be done.  For  
> instance, if one wanted to modify the created nodes (i.e. if the nodes  
> are mutable), or creating a generic Lazy set of classes capable of   
> dealing with multiple formats.
>
> Just in case anyone's wondering, I have been thinking along these  
> lines for a while re: BioPerl, Bio::Seq, and very large files... ;>
>
> chris
>   


From rozziite at gmail.com  Sat May 23 16:12:31 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sat, 23 May 2009 16:12:31 -0400
Subject: [BioRuby] GSOC: Unit testing in BioRuby
Message-ID: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com>

Hi,

How does unit testing in BioRuby works?

I created new file /lib/bio/db/phyloxml.rb and
test/unit/bio/db/test_phyloxml.rb  I also put some sample xml files in
/test/unit/data/phyloxml/ directory.

How can I access the data set in data directory from the test_phyloxml.rb
file?

Can I give path relative path to the data file? for example
"../../../data/phyloxml/phyloxml_examples.xml"

I saw other test files have this code:

"require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
"
Is this code for that purpose?  I am not really sure what this piece of code
means.

Thanks,

Diana

From mail at michaelbarton.me.uk  Sat May 23 19:00:26 2009
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Sun, 24 May 2009 00:00:26 +0100
Subject: [BioRuby] GSOC: Unit testing in BioRuby
In-Reply-To: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com>
References: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com>
Message-ID: <c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com>

Hi Diana.

You could try adding a module along these lines to your test file,
inside the TestPhyloXML module.

??module TestPyloXMLData

????bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__),
['..'] * 5)).cleanpath.to_s
????TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data',
'pyloxml')).cleanpath.to_s

????def self.example_xml
??????File.join TEST_DATA, 'phyloxml_examples.xml'
????end

??end

You can then use

TestPhyloXMLData.example_xml

To return the path to the example test data file.



The code you described in your email adds the bioruby root to the
library path so you can do

require 'bio/db/phyloxml'

at the top of your test file.

Is this any help?

Cheers

Mike


2009/5/23 Diana Jaunzeikare <rozziite at gmail.com>
>
> Hi,
>
> How does unit testing in BioRuby works?
>
> I created new file /lib/bio/db/phyloxml.rb and
> test/unit/bio/db/test_phyloxml.rb ?I also put some sample xml files in
> /test/unit/data/phyloxml/ directory.
>
> How can I access the data set in data directory from the test_phyloxml.rb
> file?
>
> Can I give path relative path to the data file? for example
> "../../../data/phyloxml/phyloxml_examples.xml"
>
> I saw other test files have this code:
>
> "require 'pathname'
> libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
> 'lib')).cleanpath.to_s
> $:.unshift(libpath) unless $:.include?(libpath)
> "
> Is this code for that purpose? ?I am not really sure what this piece of code
> means.
>
> Thanks,
>
> Diana
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From rozziite at gmail.com  Sun May 24 16:42:18 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sun, 24 May 2009 16:42:18 -0400
Subject: [BioRuby] GSOC: Unit testing in BioRuby
In-Reply-To: <c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com>
References: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com> 
	<c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com>
Message-ID: <4057d3bf0905241342x6cba94f1mf8e236cd2062199f@mail.gmail.com>

Thanks  a lot Michael! It worked.

Diana

On Sat, May 23, 2009 at 7:00 PM, Michael Barton <mail at michaelbarton.me.uk>wrote:

> Hi Diana.
>
> You could try adding a module along these lines to your test file,
> inside the TestPhyloXML module.
>
>   module TestPyloXMLData
>
>     bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__),
> ['..'] * 5)).cleanpath.to_s
>     TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data',
> 'pyloxml')).cleanpath.to_s
>
>     def self.example_xml
>       File.join TEST_DATA, 'phyloxml_examples.xml'
>     end
>
>   end
>
> You can then use
>
> TestPhyloXMLData.example_xml
>
> To return the path to the example test data file.
>
>
>
> The code you described in your email adds the bioruby root to the
> library path so you can do
>
> require 'bio/db/phyloxml'
>
> at the top of your test file.
>
> Is this any help?
>
> Cheers
>
> Mike
>
>
> 2009/5/23 Diana Jaunzeikare <rozziite at gmail.com>
> >
> > Hi,
> >
> > How does unit testing in BioRuby works?
> >
> > I created new file /lib/bio/db/phyloxml.rb and
> > test/unit/bio/db/test_phyloxml.rb  I also put some sample xml files in
> > /test/unit/data/phyloxml/ directory.
> >
> > How can I access the data set in data directory from the test_phyloxml.rb
> > file?
> >
> > Can I give path relative path to the data file? for example
> > "../../../data/phyloxml/phyloxml_examples.xml"
> >
> > I saw other test files have this code:
> >
> > "require 'pathname'
> > libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
> > 'lib')).cleanpath.to_s
> > $:.unshift(libpath) unless $:.include?(libpath)
> > "
> > Is this code for that purpose?  I am not really sure what this piece of
> code
> > means.
> >
> > Thanks,
> >
> > Diana
> > _______________________________________________
> > 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 mail at michaelbarton.me.uk  Sun May 24 18:28:07 2009
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Sun, 24 May 2009 23:28:07 +0100
Subject: [BioRuby] GSOC: Unit testing in BioRuby
In-Reply-To: <4057d3bf0905241342x6cba94f1mf8e236cd2062199f@mail.gmail.com>
References: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com> 
	<c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com> 
	<4057d3bf0905241342x6cba94f1mf8e236cd2062199f@mail.gmail.com>
Message-ID: <c27b73c0905241528t5b34ad75vb16df7daa44470fe@mail.gmail.com>

Cheers. Good luck with the rest of the project.

2009/5/24 Diana Jaunzeikare <rozziite at gmail.com>:
> Thanks? a lot Michael! It worked.
>
> Diana
>
> On Sat, May 23, 2009 at 7:00 PM, Michael Barton <mail at michaelbarton.me.uk>
> wrote:
>>
>> Hi Diana.
>>
>> You could try adding a module along these lines to your test file,
>> inside the TestPhyloXML module.
>>
>> ??module TestPyloXMLData
>>
>> ????bioruby_root ?= Pathname.new(File.join(File.dirname(__FILE__),
>> ['..'] * 5)).cleanpath.to_s
>> ????TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data',
>> 'pyloxml')).cleanpath.to_s
>>
>> ????def self.example_xml
>> ??????File.join TEST_DATA, 'phyloxml_examples.xml'
>> ????end
>>
>> ??end
>>
>> You can then use
>>
>> TestPhyloXMLData.example_xml
>>
>> To return the path to the example test data file.
>>
>>
>>
>> The code you described in your email adds the bioruby root to the
>> library path so you can do
>>
>> require 'bio/db/phyloxml'
>>
>> at the top of your test file.
>>
>> Is this any help?
>>
>> Cheers
>>
>> Mike
>>
>>
>> 2009/5/23 Diana Jaunzeikare <rozziite at gmail.com>
>> >
>> > Hi,
>> >
>> > How does unit testing in BioRuby works?
>> >
>> > I created new file /lib/bio/db/phyloxml.rb and
>> > test/unit/bio/db/test_phyloxml.rb ?I also put some sample xml files in
>> > /test/unit/data/phyloxml/ directory.
>> >
>> > How can I access the data set in data directory from the
>> > test_phyloxml.rb
>> > file?
>> >
>> > Can I give path relative path to the data file? for example
>> > "../../../data/phyloxml/phyloxml_examples.xml"
>> >
>> > I saw other test files have this code:
>> >
>> > "require 'pathname'
>> > libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
>> > 'lib')).cleanpath.to_s
>> > $:.unshift(libpath) unless $:.include?(libpath)
>> > "
>> > Is this code for that purpose? ?I am not really sure what this piece of
>> > code
>> > means.
>> >
>> > Thanks,
>> >
>> > Diana
>> > _______________________________________________
>> > 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 rozziite at gmail.com  Sun May 24 20:29:57 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sun, 24 May 2009 20:29:57 -0400
Subject: [BioRuby] [Wg-phyloinformatics] Update on phyloXML support for
	BioRuby project
In-Reply-To: <86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu> 
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org> 
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
Message-ID: <4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>

Hi all,

Since there are much more elements in PhyloXML than in Bio::Tree I propose
to make a class PhyloXMLNode which inherits from Bio::Tree::Node.

PhyloXMLNode:
# attributes from Bio::Tree::Node
* bootstrap
* bootstrap_string
* ec_number
* name
* scientific_name
* taxonomy_id

#new attributes
* id_source
* confidence [] ([] means array of elements)
* color
* node_id
* taxonomy []
* sequence [] (Bio::Sequence object)
* events
* binary_characters
* distribution []
* date
* reference []
* property []

Also, since <phylogeny> element does not only consist of <clade> elements,
but other elements also, Bio::Tree class should be extended.

PhyloXMLTree
#inherited from Bio::Tree
* options
* root

# new attributes
* rooted (boolean)
* rerootable (boolean)
* branch_length_unit
* type
* name
* id
* description
* date
* confidence []
* clade_relation []
* sequence_relation []
* property []


I think inheritance is better than creating a separate class, because then
users will be able to use Bio::Tree as before, but also being able to read
PhyloXML data files. Also then conversion from PhyloXML to other formats
will be easy since Bio::Tree class has output_newick, output_nhx,
output_phylip_distance_matrix methods.

Diana

Project Page:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby

On Thu, May 21, 2009 at 9:03 AM, Chris Fields <cjfields at illinois.edu> wrote:

> Actually, as Perl's XML::LibXML::Reader is described it almost sounds
> perfect, though I'm unsure of backtracking to a specific node in the
> tree (and thus post/pre-order of nodes). Saying that, I would be
> surprised if it weren't possible, though.
>
> chris
>
> On May 20, 2009, at 11:02 PM, Christian M Zmasek wrote:
>
> > Hi:
> >
> > Thanks for the detailed replies by Hilmar and Chris!
> > I think it is a very good idea to keep such very large trees in
> > mind, and possibly implement a solution which only loads requested
> > nodes into memory (as described by Hilmar and Chris) if there is
> > enough time left at the end of the project.
> >
> > Re "It's tricky with re: to a number of aspects, but it can be
> > done.  For  instance, if one wanted to modify the created nodes
> > (i.e. if the nodes  are mutable), or creating a generic Lazy set of
> > classes capable of   dealing with multiple formats."
> >
> > How would you do post-order or pre-order iteration of nodes?
> > Wouldn't you have to back and forth in the file?
> >
> > CZ
> >
> > Chris Fields wrote:
> >> On May 20, 2009, at 8:22 AM, Hilmar Lapp wrote:
> >>
> >>
> >>> On May 19, 2009, at 5:54 PM, Christian M Zmasek wrote:
> >>>
> >>>
> >>>> I think it is perfectly acceptable to expect to have enough memory
> >>>> to keep at least
> >>>> one tree in memory
> >>>>
> >>> Sounds like a good and perfectly reasonable starting point to me
> >>> too.
> >>> It's also the way other toolkits (such as BioPerl) work.
> >>>
> >>> Having said that, I don't find it inconceivable that we may be
> >>> working
> >>> with trees in the near future that don't fit into memory for a 1GB
> >>> RAM
> >>> machine if they are richly decorated (which is something that
> >>> phyloXML
> >>> wants to enable, isn't it?). Solving that to me though seems to be
> >>> question of writing an appropriate Tree implementation that
> >>> happens to
> >>> store most of the data on disk rather than in memory, and not an
> >>> issue
> >>> for how to write a parser. Ideally though, the parser uses a factory
> >>> for creating the (tree and/or node) objects, so that later it can be
> >>> made to use an on-disk Tree implementation simply by passing it
> >>> another factory. I.e., ideally the parser would not assume and hard-
> >>> code the Tree implementation class.
> >>>
> >>> Just my $0.02.
> >>>
> >>>     -hilmar
> >>>
> >>
> >> This could be implemented in a lazy way or using lightweight
> >> objects.   The Tree object itself contains the XML parser or a
> >> reference thereof  (probably LibXML Reader-based) and creates the
> >> relevant nodes as  needed.  The only thing needed would be some
> >> light parsing to indicate  start-end file points.
> >>
> >> It's tricky with re: to a number of aspects, but it can be done.
> >> For  instance, if one wanted to modify the created nodes (i.e. if
> >> the nodes  are mutable), or creating a generic Lazy set of classes
> >> capable of   dealing with multiple formats.
> >>
> >> Just in case anyone's wondering, I have been thinking along these
> >> lines for a while re: BioPerl, Bio::Seq, and very large files... ;>
> >>
> >> chris
> >>
> >
>
> _______________________________________________
> Wg-phyloinformatics mailing list
> Wg-phyloinformatics at nescent.org
> https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
>

From ngoto at gen-info.osaka-u.ac.jp  Mon May 25 10:04:22 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 25 May 2009 23:04:22 +0900
Subject: [BioRuby] GSOC: Unit testing in BioRuby
In-Reply-To: <c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com>
References: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com>
	<c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com>
Message-ID: <20090525140422.D258B1CBC3F4@idnmail.gen-info.osaka-u.ac.jp>

Hi,

> libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
> 'lib')).cleanpath.to_s
> $:.unshift(libpath) unless $:.include?(libpath)

>     bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__),
> ['..'] * 5)).cleanpath.to_s
>     TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data',
> 'pyloxml')).cleanpath.to_s

The magic number (in the above cases, 3 or 5) depends on
the depth of the directory of the test.

For example,

File location                      The number
test/unit/bio/test_AAA.rb               3
test/unit/bio/BBB/test_AAA.rb           4
test/unit/bio/CCC/BBB/test_AAA.rb       5

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

From czmasek at burnham.org  Mon May 25 18:16:08 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Mon, 25 May 2009 15:16:08 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
Message-ID: <4A1B18A8.1070104@burnham.org>

Hi, Diana:

What you wrote looks more or less OK.
I agree it is better to extend existing classes, as opposed to change 
them drastically.
One thing to keep in mind, is that many attributes are composed of 
multiple fields themselves, i.e. you would need to create a class for 
them (if such a class not already exists).
The most important element besides sequence, is the taxonomy class.

Since BioRuby does not contain a general purpose taxonomy class at this 
point, it might be worth spending some time in designing such a class.

I propose a taxonomy class with the following elements:
-scientific name (e.g. Nematostella vectensis)
-common name (e.g. starlet sea anemone)
-code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
-rank (e.g. species)

phyloxml also has a URI for taxonomies, but I am not sure if this is 
important for a general taxonomy class.

On the other hand, a general taxonomy class might also have
- authority (e.g. Stephenson, 1935)
- aliases []

(if these elements are considered important, they of course could be 
added to the next version of phyloxml)

What do people think about this?

Christian


Diana Jaunzeikare wrote:
> Hi all,
>
> Since there are much more elements in PhyloXML than in Bio::Tree I 
> propose to make a class PhyloXMLNode which inherits from Bio::Tree::Node.
>
> PhyloXMLNode:
> # attributes from Bio::Tree::Node
> * bootstrap
> * bootstrap_string
> * ec_number
> * name
> * scientific_name
> * taxonomy_id
>
> #new attributes
> * id_source
> * confidence [] ([] means array of elements)
> * color
> * node_id
> * taxonomy []
> * sequence [] (Bio::Sequence object)
> * events
> * binary_characters
> * distribution []
> * date
> * reference []
> * property []
>
> Also, since <phylogeny> element does not only consist of <clade> 
> elements, but other elements also, Bio::Tree class should be extended.
>
> PhyloXMLTree
> #inherited from Bio::Tree
> * options
> * root
>
> # new attributes
> * rooted (boolean)
> * rerootable (boolean)
> * branch_length_unit
> * type
> * name
> * id
> * description
> * date
> * confidence []
> * clade_relation []
> * sequence_relation []
> * property []
>
>
> I think inheritance is better than creating a separate class, because 
> then users will be able to use Bio::Tree as before, but also being 
> able to read PhyloXML data files. Also then conversion from PhyloXML 
> to other formats will be easy since Bio::Tree class has output_newick, 
> output_nhx, output_phylip_distance_matrix methods.
>
> Diana
>
> Project Page:
> https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
>
> On Thu, May 21, 2009 at 9:03 AM, Chris Fields <cjfields at illinois.edu 
> <mailto:cjfields at illinois.edu>> wrote:
>
>     Actually, as Perl's XML::LibXML::Reader is described it almost sounds
>     perfect, though I'm unsure of backtracking to a specific node in the
>     tree (and thus post/pre-order of nodes). Saying that, I would be
>     surprised if it weren't possible, though.
>
>     chris
>
>     On May 20, 2009, at 11:02 PM, Christian M Zmasek wrote:
>
>     > Hi:
>     >
>     > Thanks for the detailed replies by Hilmar and Chris!
>     > I think it is a very good idea to keep such very large trees in
>     > mind, and possibly implement a solution which only loads requested
>     > nodes into memory (as described by Hilmar and Chris) if there is
>     > enough time left at the end of the project.
>     >
>     > Re "It's tricky with re: to a number of aspects, but it can be
>     > done.  For  instance, if one wanted to modify the created nodes
>     > (i.e. if the nodes  are mutable), or creating a generic Lazy set of
>     > classes capable of   dealing with multiple formats."
>     >
>     > How would you do post-order or pre-order iteration of nodes?
>     > Wouldn't you have to back and forth in the file?
>     >
>     > CZ
>     >
>     > Chris Fields wrote:
>     >> On May 20, 2009, at 8:22 AM, Hilmar Lapp wrote:
>     >>
>     >>
>     >>> On May 19, 2009, at 5:54 PM, Christian M Zmasek wrote:
>     >>>
>     >>>
>     >>>> I think it is perfectly acceptable to expect to have enough
>     memory
>     >>>> to keep at least
>     >>>> one tree in memory
>     >>>>
>     >>> Sounds like a good and perfectly reasonable starting point to me
>     >>> too.
>     >>> It's also the way other toolkits (such as BioPerl) work.
>     >>>
>     >>> Having said that, I don't find it inconceivable that we may be
>     >>> working
>     >>> with trees in the near future that don't fit into memory for a 1GB
>     >>> RAM
>     >>> machine if they are richly decorated (which is something that
>     >>> phyloXML
>     >>> wants to enable, isn't it?). Solving that to me though seems to be
>     >>> question of writing an appropriate Tree implementation that
>     >>> happens to
>     >>> store most of the data on disk rather than in memory, and not an
>     >>> issue
>     >>> for how to write a parser. Ideally though, the parser uses a
>     factory
>     >>> for creating the (tree and/or node) objects, so that later it
>     can be
>     >>> made to use an on-disk Tree implementation simply by passing it
>     >>> another factory. I.e., ideally the parser would not assume and
>     hard-
>     >>> code the Tree implementation class.
>     >>>
>     >>> Just my $0.02.
>     >>>
>     >>>     -hilmar
>     >>>
>     >>
>     >> This could be implemented in a lazy way or using lightweight
>     >> objects.   The Tree object itself contains the XML parser or a
>     >> reference thereof  (probably LibXML Reader-based) and creates the
>     >> relevant nodes as  needed.  The only thing needed would be some
>     >> light parsing to indicate  start-end file points.
>     >>
>     >> It's tricky with re: to a number of aspects, but it can be done.
>     >> For  instance, if one wanted to modify the created nodes (i.e. if
>     >> the nodes  are mutable), or creating a generic Lazy set of classes
>     >> capable of   dealing with multiple formats.
>     >>
>     >> Just in case anyone's wondering, I have been thinking along these
>     >> lines for a while re: BioPerl, Bio::Seq, and very large files... ;>
>     >>
>     >> chris
>     >>
>     >
>
>     _______________________________________________
>     Wg-phyloinformatics mailing list
>     Wg-phyloinformatics at nescent.org
>     <mailto:Wg-phyloinformatics at nescent.org>
>     https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
>
>


From bonnalraoul at ingm.it  Tue May 26 03:25:34 2009
From: bonnalraoul at ingm.it (Raoul JP Bonnal)
Date: Tue, 26 May 2009 09:25:34 +0200
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4A1B18A8.1070104@burnham.org>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>	<4A132A8A.70102@burnham.org>	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>	<4A14D243.2010101@burnham.org>	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org>
Message-ID: <4A1B996E.2010702@ingm.it>

Christian M Zmasek ha scritto:
> I agree it is better to extend existing classes, as opposed to change 
> them drastically.
> One thing to keep in mind, is that many attributes are composed of 
> multiple fields themselves, i.e. you would need to create a class for 
> them (if such a class not already exists).
> The most important element besides sequence, is the taxonomy class.
>
> Since BioRuby does not contain a general purpose taxonomy class at 
> this point, it might be worth spending some time in designing such a 
> class.
>
> I propose a taxonomy class with the following elements:
> -scientific name (e.g. Nematostella vectensis)
> -common name (e.g. starlet sea anemone)
> -code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
> -rank (e.g. species)
>
> phyloxml also has a URI for taxonomies, but I am not sure if this is 
> important for a general taxonomy class.
>
> On the other hand, a general taxonomy class might also have
> - authority (e.g. Stephenson, 1935)
> - aliases []
> (if these elements are considered important, they of course could be 
> added to the next version of phyloxml)
>
> What do people think about this?
How other langs represent that class ? I think that having the chance to 
define a new class there is the opportunity to define a similar api 
among bio-languages.
Then, taxonomy class could be used by biosequences objects 
representing/grabbing data from biosql for example.
http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/doc/biosql-ERD.pdf

--
Ra


From francesco.strozzi at gmail.com  Tue May 26 03:48:39 2009
From: francesco.strozzi at gmail.com (Francesco Strozzi)
Date: Tue, 26 May 2009 09:48:39 +0200
Subject: [BioRuby] Miranda target scan
Message-ID: <cc542f20905260048l10c2a262q46415179cad6e8d1@mail.gmail.com>

Hi all,
I need to parse Miranda output files, after a whole genome scan for microRNA
target sites. Is there any package available to do this in BioRuby?

Thanks and cheers.

-- 

Francesco

skype: francescostrozzi

From rozziite at gmail.com  Tue May 26 08:17:24 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Tue, 26 May 2009 08:17:24 -0400
Subject: [BioRuby] Bioruby PhyloXML update
Message-ID: <4057d3bf0905260517m32167f53j5ce8ca45b43ce655@mail.gmail.com>

Hi all!

Here is what was done during community bonding period:

   - subscribed to mailing lists
   - created a blog <http://latvianlinuxgirl.blogspot.com/>
   - got familiar with Git (this was particularly useful:
   http://www.gitcasts.com/posts/railsconf-git-talk )
   - created GitHub account and forked bioruby project.
   - made first commit by adding sample phyloxml data files from
   www.phyloxml.org
   - reviewed BioPerl phyloXML implementation (also
   http://www.bioperl.org/wiki/HOWTO:Trees )
   - got familiar with libxml-ruby. Wrote simple program using both
   LibXML::XML::Reader and LibXML::XML::SAXParser to parse a simple xml file.
   - reviewed Ruby classes - Bio:Tree, Bio::Pathways
   - After discussions in mailing lists it has been agreed to use
   LibXML-ruby library, the LibXML::XML::Reader class


This weeks plan:

   - Start writing parser using LibXML::XML::Reader. It should return a
   Bio::Tree object.
   - Implement function next_tree to parse and return the next phylogeny.
   - Design Tree::Node object for containing phyloxml elements.
   - Start mapping phyloxml elements to Bio::Tree::Node, start with
   taxonomy, branch_length, scientific_name
   - Write simple unit tests.


Diana

Project page:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby

From czmasek at burnham.org  Tue May 26 22:01:28 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Tue, 26 May 2009 19:01:28 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <75226546-345B-446D-82D4-FBD5016905D8@duke.edu>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org>
	<75226546-345B-446D-82D4-FBD5016905D8@duke.edu>
Message-ID: <4A1C9EF8.9010505@burnham.org>

Hi:

It's a great idea to look at TDWG's standards.
But to me, these standards seem designed specifically for collections in museums and, not surprisingly, biodiversity applications. For the purposes of comparative genomics and related fields, these taxonomy concepts seem a little bit overkill.
In my experience, taxonomy objects which can contain a scientific name, a common name, a mnemonic, and a (typed) identifier (which could be a Uniform Resource Name (URN) or a NCBI taxonomy id) are sufficient for most applications. This is pretty much what phyloXML's taxon element contains now. 
Of course, this does not mean that a potential taxonomy class in BioRuby has to follow the concept for phyloXML.

What do you think?

Christian





Hilmar Lapp wrote:
> On May 25, 2009, at 6:16 PM, Christian M Zmasek wrote:
>
>   
>> I propose a taxonomy class with the following elements:
>> -scientific name (e.g. Nematostella vectensis)
>> -common name (e.g. starlet sea anemone)
>> -code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
>> -rank (e.g. species)
>>
>> phyloxml also has a URI for taxonomies, but I am not sure if this is
>> important for a general taxonomy class.
>>
>> On the other hand, a general taxonomy class might also have
>> - authority (e.g. Stephenson, 1935)
>> - aliases []
>>
>> (if these elements are considered important, they of course could be
>> added to the next version of phyloxml)
>>     
>
>
> Note that there is the Taxonomic Concepts Transfer Schema as a  
> ratified TDWG standard, so if you really want to have a rich  
> representation of taxonomic entities or concepts I wouldn't try to  
> roll my own.
>
> http://www.tdwg.org/standards/117/
>
> For lightweight taxonomic designation, there are taxonomic elements in  
> Darwin Core:
>
> http://wiki.tdwg.org/DarwinCore
>
> 	-hilmar
>   


From rozziite at gmail.com  Tue May 26 22:51:48 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Tue, 26 May 2009 22:51:48 -0400
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <4A1C9EF8.9010505@burnham.org>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu> 
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org> 
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com> 
	<4A1B18A8.1070104@burnham.org>
	<75226546-345B-446D-82D4-FBD5016905D8@duke.edu> 
	<4A1C9EF8.9010505@burnham.org>
Message-ID: <4057d3bf0905261951w47d17ef8l70c44d46fbbd933c@mail.gmail.com>

On Tue, May 26, 2009 at 10:01 PM, Christian M Zmasek <czmasek at burnham.org>wrote:

> Hi:
>
> It's a great idea to look at TDWG's standards.
> But to me, these standards seem designed specifically for collections in
> museums and, not surprisingly, biodiversity applications. For the purposes
> of comparative genomics and related fields, these taxonomy concepts seem a
> little bit overkill.


I totally agree that TDWG is overkill. Here is rough overview what are the
data fields in TDWG standard. I agree that most of them are irrelevant for
applications not specific to taxonomic studies.

  * MetaData
  * Specimens []
    - id
    - Institution
    - Collection
    - SpecimenItem
  * Publications []
  * TaxonNames []
    - Rank
    - Canonical Name
    - CanonicalAutorship
    - PublishedIn
    - Year
    - MicroReference
    - Typification
    - SpellingCorrectionOf
    - Basionym
    - BasedOn
    - ConservedAgainst
    - LaterHomonymesOf
    - Sanctioned
    - ReplacementNameFor
    - PublicationStatus
    - ProviderLink
    - ProviderSpecificData
  * TaxonConcepts []
    - id
    - Name
    - Rank
    - AccordingTo
    - TaxonRelationships
    - SpecimenCircumscription
    - CharacterCircumscription
    - ProviderLink
  * TaxonRelationshipAssertions

Diana


>
> In my experience, taxonomy objects which can contain a scientific name, a
> common name, a mnemonic, and a (typed) identifier (which could be a Uniform
> Resource Name (URN) or a NCBI taxonomy id) are sufficient for most
> applications. This is pretty much what phyloXML's taxon element contains
> now. Of course, this does not mean that a potential taxonomy class in
> BioRuby has to follow the concept for phyloXML.
>
> What do you think?
>
> Christian
>
>
>
>
>
>
> Hilmar Lapp wrote:
>
>> On May 25, 2009, at 6:16 PM, Christian M Zmasek wrote:
>>
>>
>>
>>> I propose a taxonomy class with the following elements:
>>> -scientific name (e.g. Nematostella vectensis)
>>> -common name (e.g. starlet sea anemone)
>>> -code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
>>> -rank (e.g. species)
>>>
>>> phyloxml also has a URI for taxonomies, but I am not sure if this is
>>> important for a general taxonomy class.
>>>
>>> On the other hand, a general taxonomy class might also have
>>> - authority (e.g. Stephenson, 1935)
>>> - aliases []
>>>
>>> (if these elements are considered important, they of course could be
>>> added to the next version of phyloxml)
>>>
>>>
>>
>>
>> Note that there is the Taxonomic Concepts Transfer Schema as a  ratified
>> TDWG standard, so if you really want to have a rich  representation of
>> taxonomic entities or concepts I wouldn't try to  roll my own.
>>
>> http://www.tdwg.org/standards/117/
>>
>> For lightweight taxonomic designation, there are taxonomic elements in
>>  Darwin Core:
>>
>> http://wiki.tdwg.org/DarwinCore
>>
>>        -hilmar
>>
>>
>
>

From rozziite at gmail.com  Tue May 26 23:02:20 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Tue, 26 May 2009 23:02:20 -0400
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <4A1B996E.2010702@ingm.it>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu> 
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org> 
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com> 
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
Message-ID: <4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>

On Tue, May 26, 2009 at 3:25 AM, Raoul JP Bonnal <bonnalraoul at ingm.it>wrote:

> Christian M Zmasek ha scritto:
>
>> I agree it is better to extend existing classes, as opposed to change them
>> drastically.
>> One thing to keep in mind, is that many attributes are composed of
>> multiple fields themselves, i.e. you would need to create a class for them
>> (if such a class not already exists).
>> The most important element besides sequence, is the taxonomy class.
>>
>> Since BioRuby does not contain a general purpose taxonomy class at this
>> point, it might be worth spending some time in designing such a class.
>>
>> I propose a taxonomy class with the following elements:
>> -scientific name (e.g. Nematostella vectensis)
>> -common name (e.g. starlet sea anemone)
>> -code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
>> -rank (e.g. species)
>>
>> phyloxml also has a URI for taxonomies, but I am not sure if this is
>> important for a general taxonomy class.
>>
>> On the other hand, a general taxonomy class might also have
>> - authority (e.g. Stephenson, 1935)
>> - aliases []
>> (if these elements are considered important, they of course could be added
>> to the next version of phyloxml)
>>
>> What do people think about this?
>>
> How other langs represent that class ? I think that having the chance to
> define a new class there is the opportunity to define a similar api among
> bio-languages.
> Then, taxonomy class could be used by biosequences objects
> representing/grabbing data from biosql for example.
>
> http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/doc/biosql-ERD.pdf
>
> --
> Ra
>
>
I looked at BioPerl and this is what I could extract and understand from
documentation (I have almost no experience with Perl)

Bio::Taxonomy:Node
  * rank (species, genus, order etc)
  * id (NCBI taxonomy id in most cases)
  * parent_id (NCBI taxonomy id in most cases)
  * genetic_code
  * mitochondrial_genetic_code
  * create_date (Date this node was created (in the database))
  * update_date (Get/Set Date this node was updated (in the database))
  * pub_date (Get/Set Date this node was published (in the database))
  * scientific_name
  * common_names []

I don't think the create_date, update_date and pub_date are necessary for
our purposes, since it is database specific information, and if you need it,
then you can go to database and get it.

I didn't found a taxonomy/taxon class in BioPython.

Here is BioJava. Its taxon class represents taxonomy information at NCBI
database. BioSQL has almost identical taxon class.

NCBITaxon Class
  * acronym
  * common name
  * equivalent name
  * genetic code
  * hidden
  * left value
  * mitogeneticcode
  * noderank
  * parent
  * rightvalue
  * scientific name
  * synonym


BioRuby has Bio::SQL::Taxon and Bio::SQL::TaxonName classes, but they are
empty.

From bonnalraoul at ingm.it  Wed May 27 03:05:28 2009
From: bonnalraoul at ingm.it (Raoul JP Bonnal)
Date: Wed, 27 May 2009 09:05:28 +0200
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
Message-ID: <4A1CE638.2030200@ingm.it>

Diana Jaunzeikare ha scritto:
>
> BioRuby has Bio::SQL::Taxon and Bio::SQL::TaxonName classes, but they 
> are empty.
That classes are "activerecord models", they map the corresponding 
tables. You do not need to specify every table column in the model 
because the columns and getter/setter method are discovered/defined  
automatically by the framework (ActiveRecord).

You can create a  Bio::Taxon class and then in the same way we did with 
BioSequence object, the generic object/class, is mapped to its real 
container.

--
Ra




From bonnalraoul at ingm.it  Wed May 27 03:30:53 2009
From: bonnalraoul at ingm.it (Raoul JP Bonnal)
Date: Wed, 27 May 2009 09:30:53 +0200
Subject: [BioRuby] Bioruby PhyloXML update
In-Reply-To: <4057d3bf0905260517m32167f53j5ce8ca45b43ce655@mail.gmail.com>
References: <4057d3bf0905260517m32167f53j5ce8ca45b43ce655@mail.gmail.com>
Message-ID: <4A1CEC2D.6010202@ingm.it>

Hi Diana,
a portability issue.
Have you guys verified if LibXML::XML is it running on JRuby ? I don't 
think so because it's implemented in C. A solution could be
this http://github.com/mguterl/libxml-jruby/tree/master but today I 
can't access to it, probably due to my network problems.

Some test, 1 year ago - last post -:
http://www.nabble.com/comparing-xml-parsing-in-JRuby-and-MRI-td16268560.html#a16268560

this is the test code - good portability example too - :
https://svn.concord.org/svn/projects/trunk/common/ruby/xml_benchmarks/xml_benchmarks.rb

Cheers.

Diana Jaunzeikare ha scritto:
> Hi all!
>
> Here is what was done during community bonding period:
>
>    - subscribed to mailing lists
>    - created a blog <http://latvianlinuxgirl.blogspot.com/>
>    - got familiar with Git (this was particularly useful:
>    http://www.gitcasts.com/posts/railsconf-git-talk )
>    - created GitHub account and forked bioruby project.
>    - made first commit by adding sample phyloxml data files from
>    www.phyloxml.org
>    - reviewed BioPerl phyloXML implementation (also
>    http://www.bioperl.org/wiki/HOWTO:Trees )
>    - got familiar with libxml-ruby. Wrote simple program using both
>    LibXML::XML::Reader and LibXML::XML::SAXParser to parse a simple xml file.
>    - reviewed Ruby classes - Bio:Tree, Bio::Pathways
>    - After discussions in mailing lists it has been agreed to use
>    LibXML-ruby library, the LibXML::XML::Reader class
>
>
> This weeks plan:
>
>    - Start writing parser using LibXML::XML::Reader. It should return a
>    Bio::Tree object.
>    - Implement function next_tree to parse and return the next phylogeny.
>    - Design Tree::Node object for containing phyloxml elements.
>    - Start mapping phyloxml elements to Bio::Tree::Node, start with
>    taxonomy, branch_length, scientific_name
>    - Write simple unit tests.
>   



From czmasek at burnham.org  Wed May 27 14:29:24 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Wed, 27 May 2009 11:29:24 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <11C49404-46B9-4D47-949B-1B7DE3CBAAF9@duke.edu>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>	<4A132A8A.70102@burnham.org>	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>	<4A14D243.2010101@burnham.org>	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>	<4A1B18A8.1070104@burnham.org>	<75226546-345B-446D-82D4-FBD5016905D8@duke.edu>	<4A1C9EF8.9010505@burnham.org>	<4057d3bf0905261951w47d17ef8l70c44d46fbbd933c@mail.gmail.com>	<24AC846C-CEAA-4D01-B1CB-A8FC8033172D@berkeleybop.org>
	<11C49404-46B9-4D47-949B-1B7DE3CBAAF9@duke.edu>
Message-ID: <4A1D8684.10701@burnham.org>

Hi:

> (BTW you will also notice that there is  
> nothing even close to the Swissprot "mnemonic" - nobody does this  
> except Swissprot - whose chief business is protein annotation, not  
> taxonomy - so you may want to consider how much significance you want  
> to give this in your object model.)
>   
Again, agreed. But in practice this  "mnemonic" is very, very useful. 
For example, it is a very handy way to create short protein 
names/identifiers which still contain human readable species information 
but are short enough the be used in a variety of alignment/phylogeny 
reconstruction programs.

> As an aside, the name of a taxon really is a proxy for a taxon  
> concept, whether that is a species or not, except that typically a  
> taxon name isn't given in full (i.e., with author, year, and  
> publication) to allow unambiguous identification. That's one of the  
> reasons why taxon identifiers are key.
Indeed.
And the taxon concept is a "science" in itself....

> BTW NCBI taxon IDs are just one  
> kind of taxon IDs. There are also Catalog of Life, ITIS, IPNI, and  
> others.
>   
Definitely. That's why the phyloxml taxonomy has a typed id.
Like so: <id type="ITIS">594569</id>.

--CZ


From czmasek at burnham.org  Wed May 27 14:41:41 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Wed, 27 May 2009 11:41:41 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
Message-ID: <4A1D8965.5050404@burnham.org>

Hi:
>
>
>
> I looked at BioPerl and this is what I could extract and understand 
> from documentation (I have almost no experience with Perl)
>
> Bio::Taxonomy:Node
>   * rank (species, genus, order etc)
>   * id (NCBI taxonomy id in most cases)
>   * parent_id (NCBI taxonomy id in most cases)
>   * genetic_code
>   * mitochondrial_genetic_code
>   * create_date (Date this node was created (in the database))
>   * update_date (Get/Set Date this node was updated (in the database))
>   * pub_date (Get/Set Date this node was published (in the database))
>   * scientific_name
>   * common_names []
This is almost a superset of what phyloxml has now.
With the exception that phyloxml has the (useful, but unloved?) "code" 
element for swiss-prot style mnomonics



>
> I don't think the create_date, update_date and pub_date are necessary 
> for our purposes, since it is database specific information, and if 
> you need it, then you can go to database and get it.
>
> I didn't found a taxonomy/taxon class in BioPython.
>
> Here is BioJava. Its taxon class represents taxonomy information at 
> NCBI database. BioSQL has almost identical taxon class.
>
> NCBITaxon Class
>   * acronym
>   * common name
>   * equivalent name
>   * genetic code
>   * hidden
>   * left value
>   * mitogeneticcode
>   * noderank
>   * parent
>   * rightvalue
>   * scientific name
>   * synonym
This seems to invite inconsitent use. What is the difference between 
"equivalent name" and "synonym"?
Similar to the BioPerl Taxonomy:Node, it has fields to store tree-like 
data (parent, rightvalue, etc.)

An interesting question related to this taxonomy issue is how to compare 
them. When are taxonomies considered equal?

--CZ





From rozziite at gmail.com  Wed May 27 22:49:58 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Wed, 27 May 2009 22:49:58 -0400
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <4A1D8965.5050404@burnham.org>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu> 
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu> 
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com> 
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it> 
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com> 
	<4A1D8965.5050404@burnham.org>
Message-ID: <4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>

On Wed, May 27, 2009 at 2:41 PM, Christian M Zmasek <czmasek at burnham.org>wrote:

> Hi:
>
>>
>>
>>
>> I looked at BioPerl and this is what I could extract and understand from
>> documentation (I have almost no experience with Perl)
>>
>> Bio::Taxonomy:Node
>>  * rank (species, genus, order etc)
>>  * id (NCBI taxonomy id in most cases)
>>  * parent_id (NCBI taxonomy id in most cases)
>>  * genetic_code
>>  * mitochondrial_genetic_code
>>  * create_date (Date this node was created (in the database))
>>  * update_date (Get/Set Date this node was updated (in the database))
>>  * pub_date (Get/Set Date this node was published (in the database))
>>  * scientific_name
>>  * common_names []
>>
> This is almost a superset of what phyloxml has now.
> With the exception that phyloxml has the (useful, but unloved?) "code"
> element for swiss-prot style mnomonics
>


What about treating "code" element as id, but with type "swiss-prot".


> I don't think the create_date, update_date and pub_date are necessary for
> our purposes, since it is database specific information, and if you need it,
> then you can go to database and get it.
>
> I didn't found a taxonomy/taxon class in BioPython.
>
> Here is BioJava. Its taxon class represents taxonomy information at NCBI
> database. BioSQL has almost identical taxon class.
>
> NCBITaxon Class
>  * acronym
>  * common name
>  * equivalent name
>  * genetic code
>  * hidden
>  * left value
>  * mitogeneticcode
>  * noderank
>  * parent
>  * rightvalue
>  * scientific name
>  * synonym
>
This seems to invite inconsitent use. What is the difference between
> "equivalent name" and "synonym"?
> Similar to the BioPerl Taxonomy:Node, it has fields to store tree-like data
> (parent, rightvalue, etc.)
>
> An interesting question related to this taxonomy issue is how to compare
> them. When are taxonomies considered equal?
>
> --CZ
>
>
>
>
>

From czmasek at burnham.org  Thu May 28 15:49:05 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Thu, 28 May 2009 12:49:05 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
	<4A1D8965.5050404@burnham.org>
	<4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
Message-ID: <4A1EEAB1.2000402@burnham.org>

Hi, Diana
> What about treating "code" element as id, but with type "swiss-prot".

I think this would be acceptable.

Christian

From czmasek at burnham.org  Thu May 28 15:51:05 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Thu, 28 May 2009 12:51:05 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
	<4A1D8965.5050404@burnham.org>
	<4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
Message-ID: <4A1EEB29.3020508@burnham.org>

Hi, Diana
> What about treating "code" element as id, but with type "swiss-prot".

I think this would be acceptable.

Christian

From czmasek at burnham.org  Thu May 28 18:52:21 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Thu, 28 May 2009 15:52:21 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
	<4A1D8965.5050404@burnham.org>
	<4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
Message-ID: <4A1F15A5.60801@burnham.org>

Hi, Diana:

Your wiki [at http://wiki.github.com/latvianlinuxgirl/bioruby] looks 
like a good idea!
I made some comments!

CZ


From rozziite at gmail.com  Sat May 30 17:27:52 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sat, 30 May 2009 17:27:52 -0400
Subject: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
Message-ID: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com>

Hi all,

So I looked more carefully at the sequence element of phyloXML and it
consists of information which cannot be mapped to Bio::Sequence object. I
suggest to have a sequence class which closely resembles phyloXML structure
and then have a method to extract relevant elements return Bio::Sequence
object.  What do you think?

Here on the left i listed phyloXML sequence tag elements and after the arrow
-> the possible corresponding attribute of Bio::Sequence
* type
** rna, dna  -> Bio::Sequence::NA -> molecule type
** aa -> Bio::Sequence::AA
* id_source (string ?) -> id_namespace
* id_ref (string ) -> entry_id
* symbol (string ?)
* accession
** source (example: "UniProtKB") ->
** id (example: "P17304") ->  primary_accession
* name (string )
* location (string ? )
* mol_seq (string) -> seq / Bio::Sequence::NA/AA
* uri
** desc (string)
** type (string )
** uri

* annotation []
** ref
** source
** evidence
** type
** desc
** confidence
** property []
** uri

* domain_architecture
** length
** domain []
*** from
*** to
*** confidence
*** id

Diana

From rozziite at gmail.com  Sat May 30 21:36:52 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sat, 30 May 2009 21:36:52 -0400
Subject: [BioRuby] Bioruby PhyloXML update
In-Reply-To: <4A1CEC2D.6010202@ingm.it>
References: <4057d3bf0905260517m32167f53j5ce8ca45b43ce655@mail.gmail.com> 
	<4A1CEC2D.6010202@ingm.it>
Message-ID: <4057d3bf0905301836k4cd0358btf87497b047a5f9d3@mail.gmail.com>

I looked at libxml-jruby and tried to install it, but i get "no such file to
load -- java" on the line "require 'java'". I have both jruby and java
installed. I also have .../jruby/bin directory in my $PATH.

Any suggestions?

Diana

On Wed, May 27, 2009 at 3:30 AM, Raoul JP Bonnal <bonnalraoul at ingm.it>wrote:

> Hi Diana,
> a portability issue.
> Have you guys verified if LibXML::XML is it running on JRuby ? I don't
> think so because it's implemented in C. A solution could be
> this http://github.com/mguterl/libxml-jruby/tree/master but today I can't
> access to it, probably due to my network problems.
>
> Some test, 1 year ago - last post -:
>
> http://www.nabble.com/comparing-xml-parsing-in-JRuby-and-MRI-td16268560.html#a16268560
>
> this is the test code - good portability example too - :
>
> https://svn.concord.org/svn/projects/trunk/common/ruby/xml_benchmarks/xml_benchmarks.rb
>
> Cheers.
>
> Diana Jaunzeikare ha scritto:
>
>> Hi all!
>>
>> Here is what was done during community bonding period:
>>
>>   - subscribed to mailing lists
>>   - created a blog <http://latvianlinuxgirl.blogspot.com/>
>>   - got familiar with Git (this was particularly useful:
>>   http://www.gitcasts.com/posts/railsconf-git-talk )
>>   - created GitHub account and forked bioruby project.
>>   - made first commit by adding sample phyloxml data files from
>>   www.phyloxml.org
>>   - reviewed BioPerl phyloXML implementation (also
>>   http://www.bioperl.org/wiki/HOWTO:Trees )
>>   - got familiar with libxml-ruby. Wrote simple program using both
>>   LibXML::XML::Reader and LibXML::XML::SAXParser to parse a simple xml
>> file.
>>   - reviewed Ruby classes - Bio:Tree, Bio::Pathways
>>   - After discussions in mailing lists it has been agreed to use
>>   LibXML-ruby library, the LibXML::XML::Reader class
>>
>>
>> This weeks plan:
>>
>>   - Start writing parser using LibXML::XML::Reader. It should return a
>>   Bio::Tree object.
>>   - Implement function next_tree to parse and return the next phylogeny.
>>   - Design Tree::Node object for containing phyloxml elements.
>>   - Start mapping phyloxml elements to Bio::Tree::Node, start with
>>   taxonomy, branch_length, scientific_name
>>   - Write simple unit tests.
>>
>>
>
>
>

From mail at michaelbarton.me.uk  Sun May 31 05:45:32 2009
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Sun, 31 May 2009 10:45:32 +0100
Subject: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
In-Reply-To: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com>
References: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com>
Message-ID: <c27b73c0905310245x198ebdb6p1f6a18d580c2e536@mail.gmail.com>

I'm not very familiar with phyloXML, but when you write sequence, do
you mean a multiple sequence alignment from which the phylogeny was
estimated? If that's the case, there is a MSA class in bioruby which
this could be mapped to perhaps?

2009/5/30 Diana Jaunzeikare <rozziite at gmail.com>:
> Hi all,
>
> So I looked more carefully at the sequence element of phyloXML and it
> consists of information which cannot be mapped to Bio::Sequence object. I
> suggest to have a sequence class which closely resembles phyloXML structure
> and then have a method to extract relevant elements return Bio::Sequence
> object. ?What do you think?
>
> Here on the left i listed phyloXML sequence tag elements and after the arrow
> -> the possible corresponding attribute of Bio::Sequence
> * type
> ** rna, dna ?-> Bio::Sequence::NA -> molecule type
> ** aa -> Bio::Sequence::AA
> * id_source (string ?) -> id_namespace
> * id_ref (string ) -> entry_id
> * symbol (string ?)
> * accession
> ** source (example: "UniProtKB") ->
> ** id (example: "P17304") -> ?primary_accession
> * name (string )
> * location (string ? )
> * mol_seq (string) -> seq / Bio::Sequence::NA/AA
> * uri
> ** desc (string)
> ** type (string )
> ** uri
>
> * annotation []
> ** ref
> ** source
> ** evidence
> ** type
> ** desc
> ** confidence
> ** property []
> ** uri
>
> * domain_architecture
> ** length
> ** domain []
> *** from
> *** to
> *** confidence
> *** id
>
> Diana
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From czmasek at burnham.org  Sun May 31 13:17:49 2009
From: czmasek at burnham.org (Christian Zmasek)
Date: Sun, 31 May 2009 10:17:49 -0700
Subject: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
In-Reply-To: <c27b73c0905310245x198ebdb6p1f6a18d580c2e536@mail.gmail.com>
References: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com>,
	<c27b73c0905310245x198ebdb6p1f6a18d580c2e536@mail.gmail.com>
Message-ID: <E4F65F2E907A6F4B8582E0E44B2505EA1ADDE2A19F@MAIL07.burnham.org>

Hi, Michael:

Good point. Actually, it is not specified. It is just a sequence associated with a node. 
In my own work, I use it for the original sequence (before the introduction of gaps, and possible trimming of columns, during and after the alignment process).
Hence, I do not think reuse of the MSA class is appropriate.

Christian

 


________________________________________
From: bioruby-bounces at lists.open-bio.org [bioruby-bounces at lists.open-bio.org] On Behalf Of Michael Barton [mail at michaelbarton.me.uk]
Sent: Sunday, May 31, 2009 2:45 AM
To: Phyloinformatics Group; bioruby at lists.open-bio.org
Subject: Re: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence

I'm not very familiar with phyloXML, but when you write sequence, do
you mean a multiple sequence alignment from which the phylogeny was
estimated? If that's the case, there is a MSA class in bioruby which
this could be mapped to perhaps?

2009/5/30 Diana Jaunzeikare <rozziite at gmail.com>:
> Hi all,
>
> So I looked more carefully at the sequence element of phyloXML and it
> consists of information which cannot be mapped to Bio::Sequence object. I
> suggest to have a sequence class which closely resembles phyloXML structure
> and then have a method to extract relevant elements return Bio::Sequence
> object.  What do you think?
>
> Here on the left i listed phyloXML sequence tag elements and after the arrow
> -> the possible corresponding attribute of Bio::Sequence
> * type
> ** rna, dna  -> Bio::Sequence::NA -> molecule type
> ** aa -> Bio::Sequence::AA
> * id_source (string ?) -> id_namespace
> * id_ref (string ) -> entry_id
> * symbol (string ?)
> * accession
> ** source (example: "UniProtKB") ->
> ** id (example: "P17304") ->  primary_accession
> * name (string )
> * location (string ? )
> * mol_seq (string) -> seq / Bio::Sequence::NA/AA
> * uri
> ** desc (string)
> ** type (string )
> ** uri
>
> * annotation []
> ** ref
> ** source
> ** evidence
> ** type
> ** desc
> ** confidence
> ** property []
> ** uri
>
> * domain_architecture
> ** length
> ** domain []
> *** from
> *** to
> *** confidence
> *** id
>
> Diana
> _______________________________________________
> 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 mail at michaelbarton.me.uk  Sun May 31 16:59:09 2009
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Sun, 31 May 2009 21:59:09 +0100
Subject: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
In-Reply-To: <E4F65F2E907A6F4B8582E0E44B2505EA1ADDE2A19F@MAIL07.burnham.org>
References: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com> 
	<c27b73c0905310245x198ebdb6p1f6a18d580c2e536@mail.gmail.com> 
	<E4F65F2E907A6F4B8582E0E44B2505EA1ADDE2A19F@MAIL07.burnham.org>
Message-ID: <c27b73c0905311359q76ba2da2pae06fdcac6de9693@mail.gmail.com>

Hi Christian

Would this mean that there is a predicted single ancestor sequence
object associated at each node in a phylogenetic tree? You could start
at a specific node and traverse to ancestor or descendant nodes, and
therefore sequences? When you write original sequence, you mean the
multiple sequence alignment?

Cheers

Mike

2009/5/31 Christian Zmasek <czmasek at burnham.org>:
> Hi, Michael:
>
> Good point. Actually, it is not specified. It is just a sequence associated with a node.
> In my own work, I use it for the original sequence (before the introduction of gaps, and possible trimming of columns, during and after the alignment process).
> Hence, I do not think reuse of the MSA class is appropriate.
>
> Christian
>
>
>
>
> ________________________________________
> From: bioruby-bounces at lists.open-bio.org [bioruby-bounces at lists.open-bio.org] On Behalf Of Michael Barton [mail at michaelbarton.me.uk]
> Sent: Sunday, May 31, 2009 2:45 AM
> To: Phyloinformatics Group; bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
>
> I'm not very familiar with phyloXML, but when you write sequence, do
> you mean a multiple sequence alignment from which the phylogeny was
> estimated? If that's the case, there is a MSA class in bioruby which
> this could be mapped to perhaps?
>
> 2009/5/30 Diana Jaunzeikare <rozziite at gmail.com>:
>> Hi all,
>>
>> So I looked more carefully at the sequence element of phyloXML and it
>> consists of information which cannot be mapped to Bio::Sequence object. I
>> suggest to have a sequence class which closely resembles phyloXML structure
>> and then have a method to extract relevant elements return Bio::Sequence
>> object. ?What do you think?
>>
>> Here on the left i listed phyloXML sequence tag elements and after the arrow
>> -> the possible corresponding attribute of Bio::Sequence
>> * type
>> ** rna, dna ?-> Bio::Sequence::NA -> molecule type
>> ** aa -> Bio::Sequence::AA
>> * id_source (string ?) -> id_namespace
>> * id_ref (string ) -> entry_id
>> * symbol (string ?)
>> * accession
>> ** source (example: "UniProtKB") ->
>> ** id (example: "P17304") -> ?primary_accession
>> * name (string )
>> * location (string ? )
>> * mol_seq (string) -> seq / Bio::Sequence::NA/AA
>> * uri
>> ** desc (string)
>> ** type (string )
>> ** uri
>>
>> * annotation []
>> ** ref
>> ** source
>> ** evidence
>> ** type
>> ** desc
>> ** confidence
>> ** property []
>> ** uri
>>
>> * domain_architecture
>> ** length
>> ** domain []
>> *** from
>> *** to
>> *** confidence
>> *** id
>>
>> Diana
>> _______________________________________________
>> 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 czmasek at burnham.org  Sun May 31 23:46:14 2009
From: czmasek at burnham.org (Christian Zmasek)
Date: Sun, 31 May 2009 20:46:14 -0700
Subject: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
In-Reply-To: <c27b73c0905311359q76ba2da2pae06fdcac6de9693@mail.gmail.com>
References: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com>
	<c27b73c0905310245x198ebdb6p1f6a18d580c2e536@mail.gmail.com>
	<E4F65F2E907A6F4B8582E0E44B2505EA1ADDE2A19F@MAIL07.burnham.org>,
	<c27b73c0905311359q76ba2da2pae06fdcac6de9693@mail.gmail.com>
Message-ID: <E4F65F2E907A6F4B8582E0E44B2505EA1ADDE2A1A4@MAIL07.burnham.org>

Hi, Mike:

In general only external nodes would have a sequence associated with them.
In the case of ancestral sequence reconstruction attempts, internal nodes might have sequences, too, though.
Please remember to none of the elements in phyloXML are mandatory.
With 'original' sequence I meant the  sequence prior to alignment.

Cheers,

Christian
 

________________________________________
From: Michael Barton [mail at michaelbarton.me.uk]
Sent: Sunday, May 31, 2009 1:59 PM
To: Christian Zmasek
Cc: Phyloinformatics Group; bioruby at lists.open-bio.org; rozziite at gmail.com
Subject: Re: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence

Hi Christian

Would this mean that there is a predicted single ancestor sequence
object associated at each node in a phylogenetic tree? You could start
at a specific node and traverse to ancestor or descendant nodes, and
therefore sequences? When you write original sequence, you mean the
multiple sequence alignment?

Cheers

Mike

2009/5/31 Christian Zmasek <czmasek at burnham.org>:
> Hi, Michael:
>
> Good point. Actually, it is not specified. It is just a sequence associated with a node.
> In my own work, I use it for the original sequence (before the introduction of gaps, and possible trimming of columns, during and after the alignment process).
> Hence, I do not think reuse of the MSA class is appropriate.
>
> Christian
>
>
>
>
> ________________________________________
> From: bioruby-bounces at lists.open-bio.org [bioruby-bounces at lists.open-bio.org] On Behalf Of Michael Barton [mail at michaelbarton.me.uk]
> Sent: Sunday, May 31, 2009 2:45 AM
> To: Phyloinformatics Group; bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
>
> I'm not very familiar with phyloXML, but when you write sequence, do
> you mean a multiple sequence alignment from which the phylogeny was
> estimated? If that's the case, there is a MSA class in bioruby which
> this could be mapped to perhaps?
>
> 2009/5/30 Diana Jaunzeikare <rozziite at gmail.com>:
>> Hi all,
>>
>> So I looked more carefully at the sequence element of phyloXML and it
>> consists of information which cannot be mapped to Bio::Sequence object. I
>> suggest to have a sequence class which closely resembles phyloXML structure
>> and then have a method to extract relevant elements return Bio::Sequence
>> object.  What do you think?
>>
>> Here on the left i listed phyloXML sequence tag elements and after the arrow
>> -> the possible corresponding attribute of Bio::Sequence
>> * type
>> ** rna, dna  -> Bio::Sequence::NA -> molecule type
>> ** aa -> Bio::Sequence::AA
>> * id_source (string ?) -> id_namespace
>> * id_ref (string ) -> entry_id
>> * symbol (string ?)
>> * accession
>> ** source (example: "UniProtKB") ->
>> ** id (example: "P17304") ->  primary_accession
>> * name (string )
>> * location (string ? )
>> * mol_seq (string) -> seq / Bio::Sequence::NA/AA
>> * uri
>> ** desc (string)
>> ** type (string )
>> ** uri
>>
>> * annotation []
>> ** ref
>> ** source
>> ** evidence
>> ** type
>> ** desc
>> ** confidence
>> ** property []
>> ** uri
>>
>> * domain_architecture
>> ** length
>> ** domain []
>> *** from
>> *** to
>> *** confidence
>> *** id
>>
>> Diana
>> _______________________________________________
>> 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 rozziite at gmail.com  Fri May  1 01:37:07 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Thu, 30 Apr 2009 21:37:07 -0400
Subject: [BioRuby] Google Summer of Code Intro: PhyloXML support in BioRuby
Message-ID: <4057d3bf0904301837r302bfb2buaa8a644c448267fa@mail.gmail.com>

Hi all,

I would like to introduce myself. My name is Diana and I have been accepted
for Google Summer of Code to implement PhyloXML support for BioRuby. I am a
junior at Smith College double majoring in Computer Science and Math. I am
interested in Bioinformatics, especially protein structure based
phylogenetics.

Here is the project abstract:

===
Phylogenetic trees are used in important applications, including
phylogenomics, phylogeography, gene function prediction, cladistics and the
study of molecular evolution. In order to foster successful analysis,
exchange, storage and reuse of phylogenetic trees and associated data, the
phyloXML format was developed. It can store all necessary information about
the phylogenetic tree, like clade, sequence, name and distance. The goal of
this project is to implement support for phyloXML in BioRuby.
===

Here is wiki:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby


Any comments are welcome!

Cheers,

Diana


From ngoto at gen-info.osaka-u.ac.jp  Wed May  6 07:56:48 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Wed, 6 May 2009 16:56:48 +0900
Subject: [BioRuby] Made a change in format10.rb
In-Reply-To: <49B4B4EA.6060401@bioreg.kyushu-u.ac.jp>
References: <49B4B4EA.6060401@bioreg.kyushu-u.ac.jp>
Message-ID: <20090506075650.37E4A1CBC4EB@idnmail.gen-info.osaka-u.ac.jp>

Hi,

Thank you for reporting a bug.

I've changed codes to support results containing two or
more query sequences.

http://github.com/bioruby/bioruby/commit/e57349594427ad1a51979c9d4e0c3efcffd160c2
http://github.com/bioruby/bioruby/commit/3d3edc44127f4fd97abcc17a859e36623facdc7c


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


On Mon, 09 Mar 2009 15:19:22 +0900
Fredrik Johansson <fredjoha at bioreg.kyushu-u.ac.jp> wrote:

> I found that Bioruby can't handle large amounts of output from Fasta. So 
> I made this change to 
> /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/fasta/format10.rb :
> 
> 6,7c6,8
> <       data.sub!(/(.*)\n\n>>>/m, '')
> <       @list = "The best scores are" + $1
> ---
>  >       border = data.index("\n\n>>>")
>  >       @list = "The best scores are" + data[0...border]
>  >       data = data[border+5..-1]
> 
> 
> The old code reported an error when the output was huge:
> RegexpError: Stack overflow in regexp matcher: /(.*)\n\n>>>/m
> 
> So I thought that maybe these lines of code should be changed in Bioruby.
> 
> Regards,
> Fredrik Johansson
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From andrew.j.grimm at gmail.com  Thu May  7 07:31:26 2009
From: andrew.j.grimm at gmail.com (Andrew Grimm)
Date: Thu, 7 May 2009 17:31:26 +1000
Subject: [BioRuby] Non deprecated way of converting a naseq to fasta?
Message-ID: <b9140daa0905070031y6effb190sc4084e08f5fd0ac0@mail.gmail.com>

The documentation for Bio::Sequence::Common talks about #to_fasta being
deprecated, in favor of Bio::Sequence #output instead. #output seems to work
for Bio::Sequence objects, but not for Bio::Sequence::NA or
Bio::Sequence::AA objects.

I can happily create a new FastaFormat object instead, but I'm wondering if
I'm doing it the right way.

Also, the wiki is still suggesting using to_fasta in some of its code
samples.

Thanks,

Andrew Grimm


From ngoto at gen-info.osaka-u.ac.jp  Wed May 13 14:55:12 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Wed, 13 May 2009 23:55:12 +0900
Subject: [BioRuby] Non deprecated way of converting a naseq to fasta?
In-Reply-To: <b9140daa0905070031y6effb190sc4084e08f5fd0ac0@mail.gmail.com>
References: <b9140daa0905070031y6effb190sc4084e08f5fd0ac0@mail.gmail.com>
Message-ID: <20090513145512.D17251CBC3CB@idnmail.gen-info.osaka-u.ac.jp>

On Thu, 7 May 2009 17:31:26 +1000
Andrew Grimm <andrew.j.grimm at gmail.com> wrote:

> The documentation for Bio::Sequence::Common talks about #to_fasta being
> deprecated, in favor of Bio::Sequence #output instead. #output seems to work
> for Bio::Sequence objects, but not for Bio::Sequence::NA or
> Bio::Sequence::AA objects.

Because the method "to_fasta" is widely and frequently used,
and alternative methods are not fully implemented, you can
still use "to_fasta".

Why "to_fasta" is planned to be deprecated is that the name
to_XXX is usually used for data class conversion in Ruby but
the current behavior of "to_fasta" is to output formatted string.

The method "to_fasta" will be deprecated in the future release,
after alternative methods are fully ready. In addition, for
smooth migration, "to_fasta" may exist as an alias (or a shortcut)
of the alternative methods for a while.

> I can happily create a new FastaFormat object instead, but I'm wondering if
> I'm doing it the right way.

To create a new Bio::Sequence object is the best way.
Bio::FastaFormat is a parser class for reading formatted string,
and is not be intended to generate formatted string.

> Also, the wiki is still suggesting using to_fasta in some of its code
> samples.

Those will be rewritten in the future.

> 
> Thanks,
> 
> Andrew Grimm
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

Thank you.

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


From pjotr.public14 at thebird.nl  Sat May 16 07:57:34 2009
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Sat, 16 May 2009 09:57:34 +0200
Subject: [BioRuby] Google Summer of Code Intro: PhyloXML support
	in	BioRuby
In-Reply-To: <4057d3bf0904301837r302bfb2buaa8a644c448267fa@mail.gmail.com>
References: <4057d3bf0904301837r302bfb2buaa8a644c448267fa@mail.gmail.com>
Message-ID: <20090516075734.GA27669@thebird.nl>

Hi Diana,

I think your contribution will be very important for BioRuby, and as
you are implementing together with others who are adding support for
BioPerl and BioPython I have great faith in you getting results.

Thank you for taking an interest. We are looking forward to your
contribution. If you have any questions on BioRuby ideas and options,
please post to this list. Note that responses can be slow, but
everyone is tracking.

Pj.

On Thu, Apr 30, 2009 at 09:37:07PM -0400, Diana Jaunzeikare wrote:
> Hi all,
> 
> I would like to introduce myself. My name is Diana and I have been accepted
> for Google Summer of Code to implement PhyloXML support for BioRuby. I am a
> junior at Smith College double majoring in Computer Science and Math. I am
> interested in Bioinformatics, especially protein structure based
> phylogenetics.
> 
> Here is the project abstract:
> 
> ===
> Phylogenetic trees are used in important applications, including
> phylogenomics, phylogeography, gene function prediction, cladistics and the
> study of molecular evolution. In order to foster successful analysis,
> exchange, storage and reuse of phylogenetic trees and associated data, the
> phyloXML format was developed. It can store all necessary information about
> the phylogenetic tree, like clade, sequence, name and distance. The goal of
> this project is to implement support for phyloXML in BioRuby.
> ===
> 
> Here is wiki:
> https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
> 
> 
> Any comments are welcome!
> 
> Cheers,
> 
> Diana
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From georgkam at gmail.com  Sat May 16 12:20:59 2009
From: georgkam at gmail.com (George Githinji)
Date: Sat, 16 May 2009 15:20:59 +0300
Subject: [BioRuby] Fwd: [BioSQL-l] BioSQL at BOSC 2009?
In-Reply-To: <320fb6e00905160512m66848611l432a81f22866b37f@mail.gmail.com>
References: <320fb6e00905160512m66848611l432a81f22866b37f@mail.gmail.com>
Message-ID: <55915f820905160520p1204f35bpbc63b6cabd936c53@mail.gmail.com>

---------- Forwarded message ----------
From: Peter <biopython at maubp.freeserve.co.uk>
Date: Sat, May 16, 2009 at 3:12 PM
Subject: [BioSQL-l] BioSQL at BOSC 2009?
To: biosql-l <biosql-l at lists.open-bio.org>
Cc: Jason Stajich <jason at bioperl.org>


Hi,

Will any of the key BioSQL people from the Bio* projects be at BOSC
(and ISMB) this year? http://open-bio.org/wiki/BOSC_2009

There will be several people from Biopython there this year, including
me and Brad Chapman who are both familiar with BioSQL.  This would be
a nice opportunity for further improving BioSQL compatibility between
the Bio* projects - something that has been suggested in the past,
e.g.

http://lists.open-bio.org/pipermail/biopython/2007-November/003893.html
http://lists.open-bio.org/pipermail/biojava-l/2007-November/006037.html

I don't follow the BioPerl, BioJava or BioRuby mailing lists - and I
doubt many of their developers follow the Biopython mailing lists.
So, rather than having any BioSQL compatibility discussions split over
individual Bio* project specific mailing lists, it seems using the
BioSQL mailing list is most appropriate.

I have CC'd a few key people just in case they are not on the BioSQL
mailing list, if I have missed anyone please forward this to them and
ask them to sign up.

Thanks,

Peter
_______________________________________________
BioSQL-l mailing list
BioSQL-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biosql-l



-- 
---------------
Sincerely
George

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


From bonnalraoul at ingm.it  Mon May 18 08:13:47 2009
From: bonnalraoul at ingm.it (Raoul JP Bonnal)
Date: Mon, 18 May 2009 10:13:47 +0200
Subject: [BioRuby] Meet Italian Developers
Message-ID: <4A1118BB.6070205@ingm.it>

Hi Guys,
I'd like to meet Italians' BioRuby developers.
Do you think would be possible to organize an informal meeting in Milan ?
Then I'd like to know how many BioRuby devs are following the list.

--
Ra



From rozziite at gmail.com  Tue May 19 21:07:59 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Tue, 19 May 2009 17:07:59 -0400
Subject: [BioRuby] Update on phyloXML support for BioRuby project
Message-ID: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>

Hi all,

I want to update you on my thoughts about this project and I have some
questions.

So, I think we have reached consensus that the best choice is libxml2-ruby
SAX based XML parser.

Since BioRuby has Tree class ( http://bioruby.org/rdoc/) it seems logical
that the parser should return a Tree class object. By using SAX parser we
avoid the problem of having whole XML file in memory, but still the
phylogenetic trees can be very large, and it might be too much to store
whole thing as a tree object in memory. This could be a little remediated by
having a function next_tree (or next_phylogeny) which would read one tree at
a time if phyloXML file has several of them (this is similar to BioPerl
implementation). I don't think the children nodes can be done in similar
fashion. Since SAX parses sequentially, to get next node (child one level
down) in the tree, whole subtree has to be parsed (in order to wait while
there is event for the end tag of that child), thus loosing on speed. Any
thoughts on this?

Also the Tree class should be extended and added method output_phyloXML
since it has methods output_newick, output_nhx.

I think in order to understand what should be returned after parsing it
would be useful to know how people use phylogenetic tree data. Here are some
I could come up,
* visualize / print
* calculate total branch length of a tree
* query info about specific nodes
* create consensus trees
Any others?

I am a little confused about the require statements in BioRuby classes. It
looks like bio/tree.rb should hold a general class, but it requires
bio/db/newick.rb, but this file in turn requires bio/tree.rb.

Thanks,

Diana

Project Page:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby


From czmasek at burnham.org  Tue May 19 21:54:18 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Tue, 19 May 2009 14:54:18 -0700
Subject: [BioRuby] Update on phyloXML support for BioRuby project
In-Reply-To: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
Message-ID: <4A132A8A.70102@burnham.org>

Hi, Diana:

I think it is a good idea to have the parser return one tree at a time, 
as opposed to returning a list of trees.

On the other hand, the same does not apply to nodes. I think it is 
perfectly acceptable to expect to have enough memory to keep at least 
one tree in memory (a good target size might be a binary tree with 
ten-thousand external nodes and 200 bytes of annotation per node, which 
according to my rough calculations would require less than 5MB).

For your tree use cases, important ones to add are:
* iteration over all nodes
* retrieval/finding of specific nodes according to some criterion (e.g. 
find all nodes for which the species is "E. coli")
* tree reconciliation (e.g. compare a gene tree to a species tree, in 
order to determine duplications on the gene tree)

In any case, all these applications/algorithms will be most time 
efficient and easiest to implement with trees which are completely in 
memory.

Re. "I am a little confused about the require statements in BioRuby 
classes. It looks like bio/tree.rb should hold a general class, but it 
requires bio/db/newick.rb, but this file in turn requires bio/tree.rb."

I am not clear about your question about this. ;)

Christian


Diana Jaunzeikare wrote:
> Hi all,
>
> I want to update you on my thoughts about this project and I have some 
> questions.
>
> So, I think we have reached consensus that the best choice is 
> libxml2-ruby SAX based XML parser.
>
> Since BioRuby has Tree class ( http://bioruby.org/rdoc/) it seems 
> logical that the parser should return a Tree class object. By using 
> SAX parser we avoid the problem of having whole XML file in memory, 
> but still the phylogenetic trees can be very large, and it might be 
> too much to store whole thing as a tree object in memory. This could 
> be a little remediated by having a function next_tree (or 
> next_phylogeny) which would read one tree at a time if phyloXML file 
> has several of them (this is similar to BioPerl implementation). I 
> don't think the children nodes can be done in similar fashion. Since 
> SAX parses sequentially, to get next node (child one level down) in 
> the tree, whole subtree has to be parsed (in order to wait while there 
> is event for the end tag of that child), thus loosing on speed. Any 
> thoughts on this?
>
> Also the Tree class should be extended and added method 
> output_phyloXML since it has methods output_newick, output_nhx.
>
> I think in order to understand what should be returned after parsing 
> it would be useful to know how people use phylogenetic tree data. Here 
> are some I could come up,
> * visualize / print
> * calculate total branch length of a tree
> * query info about specific nodes
> * create consensus trees
> Any others?
>
> I am a little confused about the require statements in BioRuby 
> classes. It looks like bio/tree.rb should hold a general class, but it 
> requires bio/db/newick.rb, but this file in turn requires bio/tree.rb.
>
> Thanks,
>
> Diana
>
> Project Page: 
> https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
>



From ngoto at gen-info.osaka-u.ac.jp  Wed May 20 06:09:17 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Wed, 20 May 2009 15:09:17 +0900
Subject: [BioRuby] Update on phyloXML support for BioRuby project
In-Reply-To: <4A132A8A.70102@burnham.org>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
Message-ID: <20090520060918.B07C71CBC3F4@idnmail.gen-info.osaka-u.ac.jp>

Hi all,

On Tue, 19 May 2009 17:07:59 -0400
Diana Jaunzeikare <rozziite at gmail.com> wrote:

> So, I think we have reached consensus that the best choice is libxml2-ruby
> SAX based XML parser.

In libxml2-ruby, I think LibXML::XML::Reader is the best choice,
because it is memory efficient than DOM and its API is simpler
than that of SAX. LibXML::XML::SAXParser is not bad, but I wonder
if the SAX's callback based API makes our codes too complex and
difficult to maintain.

> Since BioRuby has Tree class ( http://bioruby.org/rdoc/) it seems 
> logical that the parser should return a Tree class object. By using 
> SAX parser we avoid the problem of having whole XML file in memory, 

I think so.
Alternative way is to return an object of wrapper class which mimics
Bio::Tree's API. However, it may be too hard to implement such class,
and data type conversion from/to Bio::Tree is still needed even in
this case. So, I think to return a Bio::Tree object is good.

> I am a little confused about the require statements in BioRuby classes. It
> looks like bio/tree.rb should hold a general class, but it requires
> bio/db/newick.rb, but this file in turn requires bio/tree.rb.

The only reason why bio/tree.rb requires bio/db/newick.rb is
for the Newick and NHX output of the tree.  The codes will
be refactored in the future.

On Tue, 19 May 2009 14:54:18 -0700
Christian M Zmasek <czmasek at burnham.org> wrote:

> Hi, Diana:
> 
> I think it is a good idea to have the parser return one tree at a time, 
> as opposed to returning a list of trees.

I think so.

> On the other hand, the same does not apply to nodes. I think it is 
> perfectly acceptable to expect to have enough memory to keep at least 
> one tree in memory (a good target size might be a binary tree with 
> ten-thousand external nodes and 200 bytes of annotation per node, which 
> according to my rough calculations would require less than 5MB).
> 
> For your tree use cases, important ones to add are:
> * iteration over all nodes
> * retrieval/finding of specific nodes according to some criterion (e.g. 
> find all nodes for which the species is "E. coli")
> * tree reconciliation (e.g. compare a gene tree to a species tree, in 
> order to determine duplications on the gene tree)
> 
> In any case, all these applications/algorithms will be most time 
> efficient and easiest to implement with trees which are completely in 
> memory.

In addition, it is easy to implement manipulation of trees
(adding/deleting nodes and edges, etc.).

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



From rozziite at gmail.com  Wed May 20 14:51:26 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Wed, 20 May 2009 10:51:26 -0400
Subject: [BioRuby] Update on phyloXML support for BioRuby project
In-Reply-To: <20090520060918.B07C71CBC3F4@idnmail.gen-info.osaka-u.ac.jp>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<4A132A8A.70102@burnham.org>
	<20090520060918.B07C71CBC3F4@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <4057d3bf0905200751u739b37cdqe1e7d275fb82d08c@mail.gmail.com>

On Wed, May 20, 2009 at 2:09 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi all,
>
> On Tue, 19 May 2009 17:07:59 -0400
> Diana Jaunzeikare <rozziite at gmail.com> wrote:
>
> > So, I think we have reached consensus that the best choice is
> libxml2-ruby
> > SAX based XML parser.
>
> In libxml2-ruby, I think LibXML::XML::Reader is the best choice,
> because it is memory efficient than DOM and its API is simpler
> than that of SAX. LibXML::XML::SAXParser is not bad, but I wonder
> if the SAX's callback based API makes our codes too complex and
> difficult to maintain.
>

I wrote sample code using both LibXML::XML::Reader and
LibXML::XML::SAXParser and I agree that SAX's callback based API might get
very complex and hard to maintain.


>
> > Since BioRuby has Tree class ( http://bioruby.org/rdoc/) it seems
> > logical that the parser should return a Tree class object. By using
> > SAX parser we avoid the problem of having whole XML file in memory,
>
> I think so.
> Alternative way is to return an object of wrapper class which mimics
> Bio::Tree's API. However, it may be too hard to implement such class,
> and data type conversion from/to Bio::Tree is still needed even in
> this case. So, I think to return a Bio::Tree object is good.
>
> > I am a little confused about the require statements in BioRuby classes.
> It
> > looks like bio/tree.rb should hold a general class, but it requires
> > bio/db/newick.rb, but this file in turn requires bio/tree.rb.
>
> The only reason why bio/tree.rb requires bio/db/newick.rb is
> for the Newick and NHX output of the tree.  The codes will
> be refactored in the future.
>
> On Tue, 19 May 2009 14:54:18 -0700
> Christian M Zmasek <czmasek at burnham.org> wrote:
>
> > Hi, Diana:
> >
> > I think it is a good idea to have the parser return one tree at a time,
> > as opposed to returning a list of trees.
>
> I think so.
>
> > On the other hand, the same does not apply to nodes. I think it is
> > perfectly acceptable to expect to have enough memory to keep at least
> > one tree in memory (a good target size might be a binary tree with
> > ten-thousand external nodes and 200 bytes of annotation per node, which
> > according to my rough calculations would require less than 5MB).
> >
> > For your tree use cases, important ones to add are:
> > * iteration over all nodes
> > * retrieval/finding of specific nodes according to some criterion (e.g.
> > find all nodes for which the species is "E. coli")
> > * tree reconciliation (e.g. compare a gene tree to a species tree, in
> > order to determine duplications on the gene tree)
> >
> > In any case, all these applications/algorithms will be most time
> > efficient and easiest to implement with trees which are completely in
> > memory.
>
> In addition, it is easy to implement manipulation of trees
> (adding/deleting nodes and edges, etc.).
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
>


From rozziite at gmail.com  Thu May 21 02:29:40 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Wed, 20 May 2009 22:29:40 -0400
Subject: [BioRuby] [Wg-phyloinformatics] Update on phyloXML support for
	BioRubyproject
In-Reply-To: <1E5916D0F3C84F978A4A62DD89275053@NewLife>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu> 
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<1E5916D0F3C84F978A4A62DD89275053@NewLife>
Message-ID: <4057d3bf0905201929y658cb924r36c2d48f62176ed4@mail.gmail.com>

Both nexml and phyloxml are xml formats for holding information about
phylogenetic trees. Both seem to be fairly new. What's the difference? Isn't
there an ultimate goal to have one universal format for phylogenetic data
exchnage? If yes, which of these two formats would be better suitable for
it, or do they serve different purposes (as nexml is based on NEXUS format)?



My other question is about Perl phylogenetics related packages (warning: Iam
not familiar at all with BioPerl classes). Bio::TreeIO and Bio::Phylo::IO
for me seem to be doing the same task. What are the main differences between
them? If there are no fundamental differences, why there are two classes
which do the same thing.

Diana


On Wed, May 20, 2009 at 11:13 AM, Mark A. Jensen <maj at fortinbras.us> wrote:

> Should I plug my "web service blog":
>
> https://www.nescent.org/wg_evoinfo/User_talk:Mjensen#.22Streaming.22_NeXML.3F?
> Some possible useful ideas there. I've also written a flexible DOM
> implementation for Bio::Phylo, that could be
> generalized/cannibalized/stolen and
> used for iterating/streaming XML formats. It provides a standard interface
> for
> writing dom elements, but allows for easily swapping in different XML
> handling
> packages (in a BioPerly '-format => libxml' way). All in Perl I'm afraid
> (or
> proud?) to say, but it might provide ideas too. (I sent it to Rutger, but
> he
> hasn't passed judgment yet, so it's currently available 'by request to the
> author'.)
> cheers; excellent work Diana- MAJ
>
> ----- Original Message -----
> From: "Chris Fields" <cjfields at illinois.edu>
> To: "Hilmar Lapp" <hlapp at duke.edu>
> Cc: <bioruby at lists.open-bio.org>; "Phyloinformatics Group"
> <Wg-phyloinformatics at nescent.org>
> Sent: Wednesday, May 20, 2009 10:52 AM
> Subject: Re: [Wg-phyloinformatics] Update on phyloXML support for
> BioRubyproject
>
>
> >
> > On May 20, 2009, at 8:22 AM, Hilmar Lapp wrote:
> >
> >>
> >> On May 19, 2009, at 5:54 PM, Christian M Zmasek wrote:
> >>
> >>> I think it is perfectly acceptable to expect to have enough memory
> >>> to keep at least
> >>> one tree in memory
> >>
> >> Sounds like a good and perfectly reasonable starting point to me too.
> >> It's also the way other toolkits (such as BioPerl) work.
> >>
> >> Having said that, I don't find it inconceivable that we may be working
> >> with trees in the near future that don't fit into memory for a 1GB RAM
> >> machine if they are richly decorated (which is something that phyloXML
> >> wants to enable, isn't it?). Solving that to me though seems to be
> >> question of writing an appropriate Tree implementation that happens to
> >> store most of the data on disk rather than in memory, and not an issue
> >> for how to write a parser. Ideally though, the parser uses a factory
> >> for creating the (tree and/or node) objects, so that later it can be
> >> made to use an on-disk Tree implementation simply by passing it
> >> another factory. I.e., ideally the parser would not assume and hard-
> >> code the Tree implementation class.
> >>
> >> Just my $0.02.
> >>
> >> -hilmar
> >
> > This could be implemented in a lazy way or using lightweight objects.
> > The Tree object itself contains the XML parser or a reference thereof
> > (probably LibXML Reader-based) and creates the relevant nodes as
> > needed.  The only thing needed would be some light parsing to indicate
> > start-end file points.
> >
> > It's tricky with re: to a number of aspects, but it can be done.  For
> > instance, if one wanted to modify the created nodes (i.e. if the nodes
> > are mutable), or creating a generic Lazy set of classes capable of
> > dealing with multiple formats.
> >
> > Just in case anyone's wondering, I have been thinking along these
> > lines for a while re: BioPerl, Bio::Seq, and very large files... ;>
> >
> > chris
> > _______________________________________________
> > Wg-phyloinformatics mailing list
> > Wg-phyloinformatics at nescent.org
> > https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
> >
> >
>
> _______________________________________________
> Wg-phyloinformatics mailing list
> Wg-phyloinformatics at nescent.org
> https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
>


From czmasek at burnham.org  Thu May 21 04:02:11 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Wed, 20 May 2009 21:02:11 -0700
Subject: [BioRuby] [Wg-phyloinformatics] Update on phyloXML support for
 BioRuby project
In-Reply-To: <D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
Message-ID: <4A14D243.2010101@burnham.org>

Hi:

Thanks for the detailed replies by Hilmar and Chris!
I think it is a very good idea to keep such very large trees in mind, 
and possibly implement a solution which only loads requested nodes into 
memory (as described by Hilmar and Chris) if there is enough time left 
at the end of the project.

Re "It's tricky with re: to a number of aspects, but it can be done.  For  
instance, if one wanted to modify the created nodes (i.e. if the nodes  
are mutable), or creating a generic Lazy set of classes capable of   
dealing with multiple formats."

How would you do post-order or pre-order iteration of nodes? Wouldn't you have to back and forth in the file?

CZ

Chris Fields wrote:
> On May 20, 2009, at 8:22 AM, Hilmar Lapp wrote:
>
>   
>> On May 19, 2009, at 5:54 PM, Christian M Zmasek wrote:
>>
>>     
>>> I think it is perfectly acceptable to expect to have enough memory
>>> to keep at least
>>> one tree in memory
>>>       
>> Sounds like a good and perfectly reasonable starting point to me too.
>> It's also the way other toolkits (such as BioPerl) work.
>>
>> Having said that, I don't find it inconceivable that we may be working
>> with trees in the near future that don't fit into memory for a 1GB RAM
>> machine if they are richly decorated (which is something that phyloXML
>> wants to enable, isn't it?). Solving that to me though seems to be
>> question of writing an appropriate Tree implementation that happens to
>> store most of the data on disk rather than in memory, and not an issue
>> for how to write a parser. Ideally though, the parser uses a factory
>> for creating the (tree and/or node) objects, so that later it can be
>> made to use an on-disk Tree implementation simply by passing it
>> another factory. I.e., ideally the parser would not assume and hard-
>> code the Tree implementation class.
>>
>> Just my $0.02.
>>
>> 	-hilmar
>>     
>
> This could be implemented in a lazy way or using lightweight objects.   
> The Tree object itself contains the XML parser or a reference thereof  
> (probably LibXML Reader-based) and creates the relevant nodes as  
> needed.  The only thing needed would be some light parsing to indicate  
> start-end file points.
>
> It's tricky with re: to a number of aspects, but it can be done.  For  
> instance, if one wanted to modify the created nodes (i.e. if the nodes  
> are mutable), or creating a generic Lazy set of classes capable of   
> dealing with multiple formats.
>
> Just in case anyone's wondering, I have been thinking along these  
> lines for a while re: BioPerl, Bio::Seq, and very large files... ;>
>
> chris
>   



From rozziite at gmail.com  Sat May 23 20:12:31 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sat, 23 May 2009 16:12:31 -0400
Subject: [BioRuby] GSOC: Unit testing in BioRuby
Message-ID: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com>

Hi,

How does unit testing in BioRuby works?

I created new file /lib/bio/db/phyloxml.rb and
test/unit/bio/db/test_phyloxml.rb  I also put some sample xml files in
/test/unit/data/phyloxml/ directory.

How can I access the data set in data directory from the test_phyloxml.rb
file?

Can I give path relative path to the data file? for example
"../../../data/phyloxml/phyloxml_examples.xml"

I saw other test files have this code:

"require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
"
Is this code for that purpose?  I am not really sure what this piece of code
means.

Thanks,

Diana


From mail at michaelbarton.me.uk  Sat May 23 23:00:26 2009
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Sun, 24 May 2009 00:00:26 +0100
Subject: [BioRuby] GSOC: Unit testing in BioRuby
In-Reply-To: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com>
References: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com>
Message-ID: <c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com>

Hi Diana.

You could try adding a module along these lines to your test file,
inside the TestPhyloXML module.

??module TestPyloXMLData

????bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__),
['..'] * 5)).cleanpath.to_s
????TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data',
'pyloxml')).cleanpath.to_s

????def self.example_xml
??????File.join TEST_DATA, 'phyloxml_examples.xml'
????end

??end

You can then use

TestPhyloXMLData.example_xml

To return the path to the example test data file.



The code you described in your email adds the bioruby root to the
library path so you can do

require 'bio/db/phyloxml'

at the top of your test file.

Is this any help?

Cheers

Mike


2009/5/23 Diana Jaunzeikare <rozziite at gmail.com>
>
> Hi,
>
> How does unit testing in BioRuby works?
>
> I created new file /lib/bio/db/phyloxml.rb and
> test/unit/bio/db/test_phyloxml.rb ?I also put some sample xml files in
> /test/unit/data/phyloxml/ directory.
>
> How can I access the data set in data directory from the test_phyloxml.rb
> file?
>
> Can I give path relative path to the data file? for example
> "../../../data/phyloxml/phyloxml_examples.xml"
>
> I saw other test files have this code:
>
> "require 'pathname'
> libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
> 'lib')).cleanpath.to_s
> $:.unshift(libpath) unless $:.include?(libpath)
> "
> Is this code for that purpose? ?I am not really sure what this piece of code
> means.
>
> Thanks,
>
> Diana
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From rozziite at gmail.com  Sun May 24 20:42:18 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sun, 24 May 2009 16:42:18 -0400
Subject: [BioRuby] GSOC: Unit testing in BioRuby
In-Reply-To: <c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com>
References: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com> 
	<c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com>
Message-ID: <4057d3bf0905241342x6cba94f1mf8e236cd2062199f@mail.gmail.com>

Thanks  a lot Michael! It worked.

Diana

On Sat, May 23, 2009 at 7:00 PM, Michael Barton <mail at michaelbarton.me.uk>wrote:

> Hi Diana.
>
> You could try adding a module along these lines to your test file,
> inside the TestPhyloXML module.
>
>   module TestPyloXMLData
>
>     bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__),
> ['..'] * 5)).cleanpath.to_s
>     TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data',
> 'pyloxml')).cleanpath.to_s
>
>     def self.example_xml
>       File.join TEST_DATA, 'phyloxml_examples.xml'
>     end
>
>   end
>
> You can then use
>
> TestPhyloXMLData.example_xml
>
> To return the path to the example test data file.
>
>
>
> The code you described in your email adds the bioruby root to the
> library path so you can do
>
> require 'bio/db/phyloxml'
>
> at the top of your test file.
>
> Is this any help?
>
> Cheers
>
> Mike
>
>
> 2009/5/23 Diana Jaunzeikare <rozziite at gmail.com>
> >
> > Hi,
> >
> > How does unit testing in BioRuby works?
> >
> > I created new file /lib/bio/db/phyloxml.rb and
> > test/unit/bio/db/test_phyloxml.rb  I also put some sample xml files in
> > /test/unit/data/phyloxml/ directory.
> >
> > How can I access the data set in data directory from the test_phyloxml.rb
> > file?
> >
> > Can I give path relative path to the data file? for example
> > "../../../data/phyloxml/phyloxml_examples.xml"
> >
> > I saw other test files have this code:
> >
> > "require 'pathname'
> > libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
> > 'lib')).cleanpath.to_s
> > $:.unshift(libpath) unless $:.include?(libpath)
> > "
> > Is this code for that purpose?  I am not really sure what this piece of
> code
> > means.
> >
> > Thanks,
> >
> > Diana
> > _______________________________________________
> > 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 mail at michaelbarton.me.uk  Sun May 24 22:28:07 2009
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Sun, 24 May 2009 23:28:07 +0100
Subject: [BioRuby] GSOC: Unit testing in BioRuby
In-Reply-To: <4057d3bf0905241342x6cba94f1mf8e236cd2062199f@mail.gmail.com>
References: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com> 
	<c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com> 
	<4057d3bf0905241342x6cba94f1mf8e236cd2062199f@mail.gmail.com>
Message-ID: <c27b73c0905241528t5b34ad75vb16df7daa44470fe@mail.gmail.com>

Cheers. Good luck with the rest of the project.

2009/5/24 Diana Jaunzeikare <rozziite at gmail.com>:
> Thanks? a lot Michael! It worked.
>
> Diana
>
> On Sat, May 23, 2009 at 7:00 PM, Michael Barton <mail at michaelbarton.me.uk>
> wrote:
>>
>> Hi Diana.
>>
>> You could try adding a module along these lines to your test file,
>> inside the TestPhyloXML module.
>>
>> ??module TestPyloXMLData
>>
>> ????bioruby_root ?= Pathname.new(File.join(File.dirname(__FILE__),
>> ['..'] * 5)).cleanpath.to_s
>> ????TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data',
>> 'pyloxml')).cleanpath.to_s
>>
>> ????def self.example_xml
>> ??????File.join TEST_DATA, 'phyloxml_examples.xml'
>> ????end
>>
>> ??end
>>
>> You can then use
>>
>> TestPhyloXMLData.example_xml
>>
>> To return the path to the example test data file.
>>
>>
>>
>> The code you described in your email adds the bioruby root to the
>> library path so you can do
>>
>> require 'bio/db/phyloxml'
>>
>> at the top of your test file.
>>
>> Is this any help?
>>
>> Cheers
>>
>> Mike
>>
>>
>> 2009/5/23 Diana Jaunzeikare <rozziite at gmail.com>
>> >
>> > Hi,
>> >
>> > How does unit testing in BioRuby works?
>> >
>> > I created new file /lib/bio/db/phyloxml.rb and
>> > test/unit/bio/db/test_phyloxml.rb ?I also put some sample xml files in
>> > /test/unit/data/phyloxml/ directory.
>> >
>> > How can I access the data set in data directory from the
>> > test_phyloxml.rb
>> > file?
>> >
>> > Can I give path relative path to the data file? for example
>> > "../../../data/phyloxml/phyloxml_examples.xml"
>> >
>> > I saw other test files have this code:
>> >
>> > "require 'pathname'
>> > libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
>> > 'lib')).cleanpath.to_s
>> > $:.unshift(libpath) unless $:.include?(libpath)
>> > "
>> > Is this code for that purpose? ?I am not really sure what this piece of
>> > code
>> > means.
>> >
>> > Thanks,
>> >
>> > Diana
>> > _______________________________________________
>> > 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 rozziite at gmail.com  Mon May 25 00:29:57 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sun, 24 May 2009 20:29:57 -0400
Subject: [BioRuby] [Wg-phyloinformatics] Update on phyloXML support for
	BioRuby project
In-Reply-To: <86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu> 
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org> 
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
Message-ID: <4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>

Hi all,

Since there are much more elements in PhyloXML than in Bio::Tree I propose
to make a class PhyloXMLNode which inherits from Bio::Tree::Node.

PhyloXMLNode:
# attributes from Bio::Tree::Node
* bootstrap
* bootstrap_string
* ec_number
* name
* scientific_name
* taxonomy_id

#new attributes
* id_source
* confidence [] ([] means array of elements)
* color
* node_id
* taxonomy []
* sequence [] (Bio::Sequence object)
* events
* binary_characters
* distribution []
* date
* reference []
* property []

Also, since <phylogeny> element does not only consist of <clade> elements,
but other elements also, Bio::Tree class should be extended.

PhyloXMLTree
#inherited from Bio::Tree
* options
* root

# new attributes
* rooted (boolean)
* rerootable (boolean)
* branch_length_unit
* type
* name
* id
* description
* date
* confidence []
* clade_relation []
* sequence_relation []
* property []


I think inheritance is better than creating a separate class, because then
users will be able to use Bio::Tree as before, but also being able to read
PhyloXML data files. Also then conversion from PhyloXML to other formats
will be easy since Bio::Tree class has output_newick, output_nhx,
output_phylip_distance_matrix methods.

Diana

Project Page:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby

On Thu, May 21, 2009 at 9:03 AM, Chris Fields <cjfields at illinois.edu> wrote:

> Actually, as Perl's XML::LibXML::Reader is described it almost sounds
> perfect, though I'm unsure of backtracking to a specific node in the
> tree (and thus post/pre-order of nodes). Saying that, I would be
> surprised if it weren't possible, though.
>
> chris
>
> On May 20, 2009, at 11:02 PM, Christian M Zmasek wrote:
>
> > Hi:
> >
> > Thanks for the detailed replies by Hilmar and Chris!
> > I think it is a very good idea to keep such very large trees in
> > mind, and possibly implement a solution which only loads requested
> > nodes into memory (as described by Hilmar and Chris) if there is
> > enough time left at the end of the project.
> >
> > Re "It's tricky with re: to a number of aspects, but it can be
> > done.  For  instance, if one wanted to modify the created nodes
> > (i.e. if the nodes  are mutable), or creating a generic Lazy set of
> > classes capable of   dealing with multiple formats."
> >
> > How would you do post-order or pre-order iteration of nodes?
> > Wouldn't you have to back and forth in the file?
> >
> > CZ
> >
> > Chris Fields wrote:
> >> On May 20, 2009, at 8:22 AM, Hilmar Lapp wrote:
> >>
> >>
> >>> On May 19, 2009, at 5:54 PM, Christian M Zmasek wrote:
> >>>
> >>>
> >>>> I think it is perfectly acceptable to expect to have enough memory
> >>>> to keep at least
> >>>> one tree in memory
> >>>>
> >>> Sounds like a good and perfectly reasonable starting point to me
> >>> too.
> >>> It's also the way other toolkits (such as BioPerl) work.
> >>>
> >>> Having said that, I don't find it inconceivable that we may be
> >>> working
> >>> with trees in the near future that don't fit into memory for a 1GB
> >>> RAM
> >>> machine if they are richly decorated (which is something that
> >>> phyloXML
> >>> wants to enable, isn't it?). Solving that to me though seems to be
> >>> question of writing an appropriate Tree implementation that
> >>> happens to
> >>> store most of the data on disk rather than in memory, and not an
> >>> issue
> >>> for how to write a parser. Ideally though, the parser uses a factory
> >>> for creating the (tree and/or node) objects, so that later it can be
> >>> made to use an on-disk Tree implementation simply by passing it
> >>> another factory. I.e., ideally the parser would not assume and hard-
> >>> code the Tree implementation class.
> >>>
> >>> Just my $0.02.
> >>>
> >>>     -hilmar
> >>>
> >>
> >> This could be implemented in a lazy way or using lightweight
> >> objects.   The Tree object itself contains the XML parser or a
> >> reference thereof  (probably LibXML Reader-based) and creates the
> >> relevant nodes as  needed.  The only thing needed would be some
> >> light parsing to indicate  start-end file points.
> >>
> >> It's tricky with re: to a number of aspects, but it can be done.
> >> For  instance, if one wanted to modify the created nodes (i.e. if
> >> the nodes  are mutable), or creating a generic Lazy set of classes
> >> capable of   dealing with multiple formats.
> >>
> >> Just in case anyone's wondering, I have been thinking along these
> >> lines for a while re: BioPerl, Bio::Seq, and very large files... ;>
> >>
> >> chris
> >>
> >
>
> _______________________________________________
> Wg-phyloinformatics mailing list
> Wg-phyloinformatics at nescent.org
> https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
>


From ngoto at gen-info.osaka-u.ac.jp  Mon May 25 14:04:22 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 25 May 2009 23:04:22 +0900
Subject: [BioRuby] GSOC: Unit testing in BioRuby
In-Reply-To: <c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com>
References: <4057d3bf0905231312j13d44bf4s76d9f97a534fce79@mail.gmail.com>
	<c27b73c0905231600n4005c558g4debbc45370f8bb6@mail.gmail.com>
Message-ID: <20090525140422.D258B1CBC3F4@idnmail.gen-info.osaka-u.ac.jp>

Hi,

> libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
> 'lib')).cleanpath.to_s
> $:.unshift(libpath) unless $:.include?(libpath)

>     bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__),
> ['..'] * 5)).cleanpath.to_s
>     TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data',
> 'pyloxml')).cleanpath.to_s

The magic number (in the above cases, 3 or 5) depends on
the depth of the directory of the test.

For example,

File location                      The number
test/unit/bio/test_AAA.rb               3
test/unit/bio/BBB/test_AAA.rb           4
test/unit/bio/CCC/BBB/test_AAA.rb       5

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


From czmasek at burnham.org  Mon May 25 22:16:08 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Mon, 25 May 2009 15:16:08 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
Message-ID: <4A1B18A8.1070104@burnham.org>

Hi, Diana:

What you wrote looks more or less OK.
I agree it is better to extend existing classes, as opposed to change 
them drastically.
One thing to keep in mind, is that many attributes are composed of 
multiple fields themselves, i.e. you would need to create a class for 
them (if such a class not already exists).
The most important element besides sequence, is the taxonomy class.

Since BioRuby does not contain a general purpose taxonomy class at this 
point, it might be worth spending some time in designing such a class.

I propose a taxonomy class with the following elements:
-scientific name (e.g. Nematostella vectensis)
-common name (e.g. starlet sea anemone)
-code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
-rank (e.g. species)

phyloxml also has a URI for taxonomies, but I am not sure if this is 
important for a general taxonomy class.

On the other hand, a general taxonomy class might also have
- authority (e.g. Stephenson, 1935)
- aliases []

(if these elements are considered important, they of course could be 
added to the next version of phyloxml)

What do people think about this?

Christian


Diana Jaunzeikare wrote:
> Hi all,
>
> Since there are much more elements in PhyloXML than in Bio::Tree I 
> propose to make a class PhyloXMLNode which inherits from Bio::Tree::Node.
>
> PhyloXMLNode:
> # attributes from Bio::Tree::Node
> * bootstrap
> * bootstrap_string
> * ec_number
> * name
> * scientific_name
> * taxonomy_id
>
> #new attributes
> * id_source
> * confidence [] ([] means array of elements)
> * color
> * node_id
> * taxonomy []
> * sequence [] (Bio::Sequence object)
> * events
> * binary_characters
> * distribution []
> * date
> * reference []
> * property []
>
> Also, since <phylogeny> element does not only consist of <clade> 
> elements, but other elements also, Bio::Tree class should be extended.
>
> PhyloXMLTree
> #inherited from Bio::Tree
> * options
> * root
>
> # new attributes
> * rooted (boolean)
> * rerootable (boolean)
> * branch_length_unit
> * type
> * name
> * id
> * description
> * date
> * confidence []
> * clade_relation []
> * sequence_relation []
> * property []
>
>
> I think inheritance is better than creating a separate class, because 
> then users will be able to use Bio::Tree as before, but also being 
> able to read PhyloXML data files. Also then conversion from PhyloXML 
> to other formats will be easy since Bio::Tree class has output_newick, 
> output_nhx, output_phylip_distance_matrix methods.
>
> Diana
>
> Project Page:
> https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
>
> On Thu, May 21, 2009 at 9:03 AM, Chris Fields <cjfields at illinois.edu 
> <mailto:cjfields at illinois.edu>> wrote:
>
>     Actually, as Perl's XML::LibXML::Reader is described it almost sounds
>     perfect, though I'm unsure of backtracking to a specific node in the
>     tree (and thus post/pre-order of nodes). Saying that, I would be
>     surprised if it weren't possible, though.
>
>     chris
>
>     On May 20, 2009, at 11:02 PM, Christian M Zmasek wrote:
>
>     > Hi:
>     >
>     > Thanks for the detailed replies by Hilmar and Chris!
>     > I think it is a very good idea to keep such very large trees in
>     > mind, and possibly implement a solution which only loads requested
>     > nodes into memory (as described by Hilmar and Chris) if there is
>     > enough time left at the end of the project.
>     >
>     > Re "It's tricky with re: to a number of aspects, but it can be
>     > done.  For  instance, if one wanted to modify the created nodes
>     > (i.e. if the nodes  are mutable), or creating a generic Lazy set of
>     > classes capable of   dealing with multiple formats."
>     >
>     > How would you do post-order or pre-order iteration of nodes?
>     > Wouldn't you have to back and forth in the file?
>     >
>     > CZ
>     >
>     > Chris Fields wrote:
>     >> On May 20, 2009, at 8:22 AM, Hilmar Lapp wrote:
>     >>
>     >>
>     >>> On May 19, 2009, at 5:54 PM, Christian M Zmasek wrote:
>     >>>
>     >>>
>     >>>> I think it is perfectly acceptable to expect to have enough
>     memory
>     >>>> to keep at least
>     >>>> one tree in memory
>     >>>>
>     >>> Sounds like a good and perfectly reasonable starting point to me
>     >>> too.
>     >>> It's also the way other toolkits (such as BioPerl) work.
>     >>>
>     >>> Having said that, I don't find it inconceivable that we may be
>     >>> working
>     >>> with trees in the near future that don't fit into memory for a 1GB
>     >>> RAM
>     >>> machine if they are richly decorated (which is something that
>     >>> phyloXML
>     >>> wants to enable, isn't it?). Solving that to me though seems to be
>     >>> question of writing an appropriate Tree implementation that
>     >>> happens to
>     >>> store most of the data on disk rather than in memory, and not an
>     >>> issue
>     >>> for how to write a parser. Ideally though, the parser uses a
>     factory
>     >>> for creating the (tree and/or node) objects, so that later it
>     can be
>     >>> made to use an on-disk Tree implementation simply by passing it
>     >>> another factory. I.e., ideally the parser would not assume and
>     hard-
>     >>> code the Tree implementation class.
>     >>>
>     >>> Just my $0.02.
>     >>>
>     >>>     -hilmar
>     >>>
>     >>
>     >> This could be implemented in a lazy way or using lightweight
>     >> objects.   The Tree object itself contains the XML parser or a
>     >> reference thereof  (probably LibXML Reader-based) and creates the
>     >> relevant nodes as  needed.  The only thing needed would be some
>     >> light parsing to indicate  start-end file points.
>     >>
>     >> It's tricky with re: to a number of aspects, but it can be done.
>     >> For  instance, if one wanted to modify the created nodes (i.e. if
>     >> the nodes  are mutable), or creating a generic Lazy set of classes
>     >> capable of   dealing with multiple formats.
>     >>
>     >> Just in case anyone's wondering, I have been thinking along these
>     >> lines for a while re: BioPerl, Bio::Seq, and very large files... ;>
>     >>
>     >> chris
>     >>
>     >
>
>     _______________________________________________
>     Wg-phyloinformatics mailing list
>     Wg-phyloinformatics at nescent.org
>     <mailto:Wg-phyloinformatics at nescent.org>
>     https://lists.nescent.org/mailman/listinfo/wg-phyloinformatics
>
>



From bonnalraoul at ingm.it  Tue May 26 07:25:34 2009
From: bonnalraoul at ingm.it (Raoul JP Bonnal)
Date: Tue, 26 May 2009 09:25:34 +0200
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4A1B18A8.1070104@burnham.org>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>	<4A132A8A.70102@burnham.org>	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>	<4A14D243.2010101@burnham.org>	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org>
Message-ID: <4A1B996E.2010702@ingm.it>

Christian M Zmasek ha scritto:
> I agree it is better to extend existing classes, as opposed to change 
> them drastically.
> One thing to keep in mind, is that many attributes are composed of 
> multiple fields themselves, i.e. you would need to create a class for 
> them (if such a class not already exists).
> The most important element besides sequence, is the taxonomy class.
>
> Since BioRuby does not contain a general purpose taxonomy class at 
> this point, it might be worth spending some time in designing such a 
> class.
>
> I propose a taxonomy class with the following elements:
> -scientific name (e.g. Nematostella vectensis)
> -common name (e.g. starlet sea anemone)
> -code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
> -rank (e.g. species)
>
> phyloxml also has a URI for taxonomies, but I am not sure if this is 
> important for a general taxonomy class.
>
> On the other hand, a general taxonomy class might also have
> - authority (e.g. Stephenson, 1935)
> - aliases []
> (if these elements are considered important, they of course could be 
> added to the next version of phyloxml)
>
> What do people think about this?
How other langs represent that class ? I think that having the chance to 
define a new class there is the opportunity to define a similar api 
among bio-languages.
Then, taxonomy class could be used by biosequences objects 
representing/grabbing data from biosql for example.
http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/doc/biosql-ERD.pdf

--
Ra



From francesco.strozzi at gmail.com  Tue May 26 07:48:39 2009
From: francesco.strozzi at gmail.com (Francesco Strozzi)
Date: Tue, 26 May 2009 09:48:39 +0200
Subject: [BioRuby] Miranda target scan
Message-ID: <cc542f20905260048l10c2a262q46415179cad6e8d1@mail.gmail.com>

Hi all,
I need to parse Miranda output files, after a whole genome scan for microRNA
target sites. Is there any package available to do this in BioRuby?

Thanks and cheers.

-- 

Francesco

skype: francescostrozzi


From rozziite at gmail.com  Tue May 26 12:17:24 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Tue, 26 May 2009 08:17:24 -0400
Subject: [BioRuby] Bioruby PhyloXML update
Message-ID: <4057d3bf0905260517m32167f53j5ce8ca45b43ce655@mail.gmail.com>

Hi all!

Here is what was done during community bonding period:

   - subscribed to mailing lists
   - created a blog <http://latvianlinuxgirl.blogspot.com/>
   - got familiar with Git (this was particularly useful:
   http://www.gitcasts.com/posts/railsconf-git-talk )
   - created GitHub account and forked bioruby project.
   - made first commit by adding sample phyloxml data files from
   www.phyloxml.org
   - reviewed BioPerl phyloXML implementation (also
   http://www.bioperl.org/wiki/HOWTO:Trees )
   - got familiar with libxml-ruby. Wrote simple program using both
   LibXML::XML::Reader and LibXML::XML::SAXParser to parse a simple xml file.
   - reviewed Ruby classes - Bio:Tree, Bio::Pathways
   - After discussions in mailing lists it has been agreed to use
   LibXML-ruby library, the LibXML::XML::Reader class


This weeks plan:

   - Start writing parser using LibXML::XML::Reader. It should return a
   Bio::Tree object.
   - Implement function next_tree to parse and return the next phylogeny.
   - Design Tree::Node object for containing phyloxml elements.
   - Start mapping phyloxml elements to Bio::Tree::Node, start with
   taxonomy, branch_length, scientific_name
   - Write simple unit tests.


Diana

Project page:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby


From czmasek at burnham.org  Wed May 27 02:01:28 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Tue, 26 May 2009 19:01:28 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <75226546-345B-446D-82D4-FBD5016905D8@duke.edu>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org>
	<75226546-345B-446D-82D4-FBD5016905D8@duke.edu>
Message-ID: <4A1C9EF8.9010505@burnham.org>

Hi:

It's a great idea to look at TDWG's standards.
But to me, these standards seem designed specifically for collections in museums and, not surprisingly, biodiversity applications. For the purposes of comparative genomics and related fields, these taxonomy concepts seem a little bit overkill.
In my experience, taxonomy objects which can contain a scientific name, a common name, a mnemonic, and a (typed) identifier (which could be a Uniform Resource Name (URN) or a NCBI taxonomy id) are sufficient for most applications. This is pretty much what phyloXML's taxon element contains now. 
Of course, this does not mean that a potential taxonomy class in BioRuby has to follow the concept for phyloXML.

What do you think?

Christian





Hilmar Lapp wrote:
> On May 25, 2009, at 6:16 PM, Christian M Zmasek wrote:
>
>   
>> I propose a taxonomy class with the following elements:
>> -scientific name (e.g. Nematostella vectensis)
>> -common name (e.g. starlet sea anemone)
>> -code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
>> -rank (e.g. species)
>>
>> phyloxml also has a URI for taxonomies, but I am not sure if this is
>> important for a general taxonomy class.
>>
>> On the other hand, a general taxonomy class might also have
>> - authority (e.g. Stephenson, 1935)
>> - aliases []
>>
>> (if these elements are considered important, they of course could be
>> added to the next version of phyloxml)
>>     
>
>
> Note that there is the Taxonomic Concepts Transfer Schema as a  
> ratified TDWG standard, so if you really want to have a rich  
> representation of taxonomic entities or concepts I wouldn't try to  
> roll my own.
>
> http://www.tdwg.org/standards/117/
>
> For lightweight taxonomic designation, there are taxonomic elements in  
> Darwin Core:
>
> http://wiki.tdwg.org/DarwinCore
>
> 	-hilmar
>   



From rozziite at gmail.com  Wed May 27 02:51:48 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Tue, 26 May 2009 22:51:48 -0400
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <4A1C9EF8.9010505@burnham.org>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu> 
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org> 
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com> 
	<4A1B18A8.1070104@burnham.org>
	<75226546-345B-446D-82D4-FBD5016905D8@duke.edu> 
	<4A1C9EF8.9010505@burnham.org>
Message-ID: <4057d3bf0905261951w47d17ef8l70c44d46fbbd933c@mail.gmail.com>

On Tue, May 26, 2009 at 10:01 PM, Christian M Zmasek <czmasek at burnham.org>wrote:

> Hi:
>
> It's a great idea to look at TDWG's standards.
> But to me, these standards seem designed specifically for collections in
> museums and, not surprisingly, biodiversity applications. For the purposes
> of comparative genomics and related fields, these taxonomy concepts seem a
> little bit overkill.


I totally agree that TDWG is overkill. Here is rough overview what are the
data fields in TDWG standard. I agree that most of them are irrelevant for
applications not specific to taxonomic studies.

  * MetaData
  * Specimens []
    - id
    - Institution
    - Collection
    - SpecimenItem
  * Publications []
  * TaxonNames []
    - Rank
    - Canonical Name
    - CanonicalAutorship
    - PublishedIn
    - Year
    - MicroReference
    - Typification
    - SpellingCorrectionOf
    - Basionym
    - BasedOn
    - ConservedAgainst
    - LaterHomonymesOf
    - Sanctioned
    - ReplacementNameFor
    - PublicationStatus
    - ProviderLink
    - ProviderSpecificData
  * TaxonConcepts []
    - id
    - Name
    - Rank
    - AccordingTo
    - TaxonRelationships
    - SpecimenCircumscription
    - CharacterCircumscription
    - ProviderLink
  * TaxonRelationshipAssertions

Diana


>
> In my experience, taxonomy objects which can contain a scientific name, a
> common name, a mnemonic, and a (typed) identifier (which could be a Uniform
> Resource Name (URN) or a NCBI taxonomy id) are sufficient for most
> applications. This is pretty much what phyloXML's taxon element contains
> now. Of course, this does not mean that a potential taxonomy class in
> BioRuby has to follow the concept for phyloXML.
>
> What do you think?
>
> Christian
>
>
>
>
>
>
> Hilmar Lapp wrote:
>
>> On May 25, 2009, at 6:16 PM, Christian M Zmasek wrote:
>>
>>
>>
>>> I propose a taxonomy class with the following elements:
>>> -scientific name (e.g. Nematostella vectensis)
>>> -common name (e.g. starlet sea anemone)
>>> -code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
>>> -rank (e.g. species)
>>>
>>> phyloxml also has a URI for taxonomies, but I am not sure if this is
>>> important for a general taxonomy class.
>>>
>>> On the other hand, a general taxonomy class might also have
>>> - authority (e.g. Stephenson, 1935)
>>> - aliases []
>>>
>>> (if these elements are considered important, they of course could be
>>> added to the next version of phyloxml)
>>>
>>>
>>
>>
>> Note that there is the Taxonomic Concepts Transfer Schema as a  ratified
>> TDWG standard, so if you really want to have a rich  representation of
>> taxonomic entities or concepts I wouldn't try to  roll my own.
>>
>> http://www.tdwg.org/standards/117/
>>
>> For lightweight taxonomic designation, there are taxonomic elements in
>>  Darwin Core:
>>
>> http://wiki.tdwg.org/DarwinCore
>>
>>        -hilmar
>>
>>
>
>


From rozziite at gmail.com  Wed May 27 03:02:20 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Tue, 26 May 2009 23:02:20 -0400
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <4A1B996E.2010702@ingm.it>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu> 
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org> 
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com> 
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
Message-ID: <4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>

On Tue, May 26, 2009 at 3:25 AM, Raoul JP Bonnal <bonnalraoul at ingm.it>wrote:

> Christian M Zmasek ha scritto:
>
>> I agree it is better to extend existing classes, as opposed to change them
>> drastically.
>> One thing to keep in mind, is that many attributes are composed of
>> multiple fields themselves, i.e. you would need to create a class for them
>> (if such a class not already exists).
>> The most important element besides sequence, is the taxonomy class.
>>
>> Since BioRuby does not contain a general purpose taxonomy class at this
>> point, it might be worth spending some time in designing such a class.
>>
>> I propose a taxonomy class with the following elements:
>> -scientific name (e.g. Nematostella vectensis)
>> -common name (e.g. starlet sea anemone)
>> -code (or mnemonic, as used by swiss-port) (e.g. NEMVE)
>> -rank (e.g. species)
>>
>> phyloxml also has a URI for taxonomies, but I am not sure if this is
>> important for a general taxonomy class.
>>
>> On the other hand, a general taxonomy class might also have
>> - authority (e.g. Stephenson, 1935)
>> - aliases []
>> (if these elements are considered important, they of course could be added
>> to the next version of phyloxml)
>>
>> What do people think about this?
>>
> How other langs represent that class ? I think that having the chance to
> define a new class there is the opportunity to define a similar api among
> bio-languages.
> Then, taxonomy class could be used by biosequences objects
> representing/grabbing data from biosql for example.
>
> http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/doc/biosql-ERD.pdf
>
> --
> Ra
>
>
I looked at BioPerl and this is what I could extract and understand from
documentation (I have almost no experience with Perl)

Bio::Taxonomy:Node
  * rank (species, genus, order etc)
  * id (NCBI taxonomy id in most cases)
  * parent_id (NCBI taxonomy id in most cases)
  * genetic_code
  * mitochondrial_genetic_code
  * create_date (Date this node was created (in the database))
  * update_date (Get/Set Date this node was updated (in the database))
  * pub_date (Get/Set Date this node was published (in the database))
  * scientific_name
  * common_names []

I don't think the create_date, update_date and pub_date are necessary for
our purposes, since it is database specific information, and if you need it,
then you can go to database and get it.

I didn't found a taxonomy/taxon class in BioPython.

Here is BioJava. Its taxon class represents taxonomy information at NCBI
database. BioSQL has almost identical taxon class.

NCBITaxon Class
  * acronym
  * common name
  * equivalent name
  * genetic code
  * hidden
  * left value
  * mitogeneticcode
  * noderank
  * parent
  * rightvalue
  * scientific name
  * synonym


BioRuby has Bio::SQL::Taxon and Bio::SQL::TaxonName classes, but they are
empty.


From bonnalraoul at ingm.it  Wed May 27 07:05:28 2009
From: bonnalraoul at ingm.it (Raoul JP Bonnal)
Date: Wed, 27 May 2009 09:05:28 +0200
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
Message-ID: <4A1CE638.2030200@ingm.it>

Diana Jaunzeikare ha scritto:
>
> BioRuby has Bio::SQL::Taxon and Bio::SQL::TaxonName classes, but they 
> are empty.
That classes are "activerecord models", they map the corresponding 
tables. You do not need to specify every table column in the model 
because the columns and getter/setter method are discovered/defined  
automatically by the framework (ActiveRecord).

You can create a  Bio::Taxon class and then in the same way we did with 
BioSequence object, the generic object/class, is mapped to its real 
container.

--
Ra





From bonnalraoul at ingm.it  Wed May 27 07:30:53 2009
From: bonnalraoul at ingm.it (Raoul JP Bonnal)
Date: Wed, 27 May 2009 09:30:53 +0200
Subject: [BioRuby] Bioruby PhyloXML update
In-Reply-To: <4057d3bf0905260517m32167f53j5ce8ca45b43ce655@mail.gmail.com>
References: <4057d3bf0905260517m32167f53j5ce8ca45b43ce655@mail.gmail.com>
Message-ID: <4A1CEC2D.6010202@ingm.it>

Hi Diana,
a portability issue.
Have you guys verified if LibXML::XML is it running on JRuby ? I don't 
think so because it's implemented in C. A solution could be
this http://github.com/mguterl/libxml-jruby/tree/master but today I 
can't access to it, probably due to my network problems.

Some test, 1 year ago - last post -:
http://www.nabble.com/comparing-xml-parsing-in-JRuby-and-MRI-td16268560.html#a16268560

this is the test code - good portability example too - :
https://svn.concord.org/svn/projects/trunk/common/ruby/xml_benchmarks/xml_benchmarks.rb

Cheers.

Diana Jaunzeikare ha scritto:
> Hi all!
>
> Here is what was done during community bonding period:
>
>    - subscribed to mailing lists
>    - created a blog <http://latvianlinuxgirl.blogspot.com/>
>    - got familiar with Git (this was particularly useful:
>    http://www.gitcasts.com/posts/railsconf-git-talk )
>    - created GitHub account and forked bioruby project.
>    - made first commit by adding sample phyloxml data files from
>    www.phyloxml.org
>    - reviewed BioPerl phyloXML implementation (also
>    http://www.bioperl.org/wiki/HOWTO:Trees )
>    - got familiar with libxml-ruby. Wrote simple program using both
>    LibXML::XML::Reader and LibXML::XML::SAXParser to parse a simple xml file.
>    - reviewed Ruby classes - Bio:Tree, Bio::Pathways
>    - After discussions in mailing lists it has been agreed to use
>    LibXML-ruby library, the LibXML::XML::Reader class
>
>
> This weeks plan:
>
>    - Start writing parser using LibXML::XML::Reader. It should return a
>    Bio::Tree object.
>    - Implement function next_tree to parse and return the next phylogeny.
>    - Design Tree::Node object for containing phyloxml elements.
>    - Start mapping phyloxml elements to Bio::Tree::Node, start with
>    taxonomy, branch_length, scientific_name
>    - Write simple unit tests.
>   




From czmasek at burnham.org  Wed May 27 18:29:24 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Wed, 27 May 2009 11:29:24 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <11C49404-46B9-4D47-949B-1B7DE3CBAAF9@duke.edu>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>	<4A132A8A.70102@burnham.org>	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>	<4A14D243.2010101@burnham.org>	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>	<4A1B18A8.1070104@burnham.org>	<75226546-345B-446D-82D4-FBD5016905D8@duke.edu>	<4A1C9EF8.9010505@burnham.org>	<4057d3bf0905261951w47d17ef8l70c44d46fbbd933c@mail.gmail.com>	<24AC846C-CEAA-4D01-B1CB-A8FC8033172D@berkeleybop.org>
	<11C49404-46B9-4D47-949B-1B7DE3CBAAF9@duke.edu>
Message-ID: <4A1D8684.10701@burnham.org>

Hi:

> (BTW you will also notice that there is  
> nothing even close to the Swissprot "mnemonic" - nobody does this  
> except Swissprot - whose chief business is protein annotation, not  
> taxonomy - so you may want to consider how much significance you want  
> to give this in your object model.)
>   
Again, agreed. But in practice this  "mnemonic" is very, very useful. 
For example, it is a very handy way to create short protein 
names/identifiers which still contain human readable species information 
but are short enough the be used in a variety of alignment/phylogeny 
reconstruction programs.

> As an aside, the name of a taxon really is a proxy for a taxon  
> concept, whether that is a species or not, except that typically a  
> taxon name isn't given in full (i.e., with author, year, and  
> publication) to allow unambiguous identification. That's one of the  
> reasons why taxon identifiers are key.
Indeed.
And the taxon concept is a "science" in itself....

> BTW NCBI taxon IDs are just one  
> kind of taxon IDs. There are also Catalog of Life, ITIS, IPNI, and  
> others.
>   
Definitely. That's why the phyloxml taxonomy has a typed id.
Like so: <id type="ITIS">594569</id>.

--CZ



From czmasek at burnham.org  Wed May 27 18:41:41 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Wed, 27 May 2009 11:41:41 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<4A132A8A.70102@burnham.org>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
Message-ID: <4A1D8965.5050404@burnham.org>

Hi:
>
>
>
> I looked at BioPerl and this is what I could extract and understand 
> from documentation (I have almost no experience with Perl)
>
> Bio::Taxonomy:Node
>   * rank (species, genus, order etc)
>   * id (NCBI taxonomy id in most cases)
>   * parent_id (NCBI taxonomy id in most cases)
>   * genetic_code
>   * mitochondrial_genetic_code
>   * create_date (Date this node was created (in the database))
>   * update_date (Get/Set Date this node was updated (in the database))
>   * pub_date (Get/Set Date this node was published (in the database))
>   * scientific_name
>   * common_names []
This is almost a superset of what phyloxml has now.
With the exception that phyloxml has the (useful, but unloved?) "code" 
element for swiss-prot style mnomonics



>
> I don't think the create_date, update_date and pub_date are necessary 
> for our purposes, since it is database specific information, and if 
> you need it, then you can go to database and get it.
>
> I didn't found a taxonomy/taxon class in BioPython.
>
> Here is BioJava. Its taxon class represents taxonomy information at 
> NCBI database. BioSQL has almost identical taxon class.
>
> NCBITaxon Class
>   * acronym
>   * common name
>   * equivalent name
>   * genetic code
>   * hidden
>   * left value
>   * mitogeneticcode
>   * noderank
>   * parent
>   * rightvalue
>   * scientific name
>   * synonym
This seems to invite inconsitent use. What is the difference between 
"equivalent name" and "synonym"?
Similar to the BioPerl Taxonomy:Node, it has fields to store tree-like 
data (parent, rightvalue, etc.)

An interesting question related to this taxonomy issue is how to compare 
them. When are taxonomies considered equal?

--CZ






From rozziite at gmail.com  Thu May 28 02:49:58 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Wed, 27 May 2009 22:49:58 -0400
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
	support
In-Reply-To: <4A1D8965.5050404@burnham.org>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com> 
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu> 
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu> 
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com> 
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it> 
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com> 
	<4A1D8965.5050404@burnham.org>
Message-ID: <4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>

On Wed, May 27, 2009 at 2:41 PM, Christian M Zmasek <czmasek at burnham.org>wrote:

> Hi:
>
>>
>>
>>
>> I looked at BioPerl and this is what I could extract and understand from
>> documentation (I have almost no experience with Perl)
>>
>> Bio::Taxonomy:Node
>>  * rank (species, genus, order etc)
>>  * id (NCBI taxonomy id in most cases)
>>  * parent_id (NCBI taxonomy id in most cases)
>>  * genetic_code
>>  * mitochondrial_genetic_code
>>  * create_date (Date this node was created (in the database))
>>  * update_date (Get/Set Date this node was updated (in the database))
>>  * pub_date (Get/Set Date this node was published (in the database))
>>  * scientific_name
>>  * common_names []
>>
> This is almost a superset of what phyloxml has now.
> With the exception that phyloxml has the (useful, but unloved?) "code"
> element for swiss-prot style mnomonics
>


What about treating "code" element as id, but with type "swiss-prot".


> I don't think the create_date, update_date and pub_date are necessary for
> our purposes, since it is database specific information, and if you need it,
> then you can go to database and get it.
>
> I didn't found a taxonomy/taxon class in BioPython.
>
> Here is BioJava. Its taxon class represents taxonomy information at NCBI
> database. BioSQL has almost identical taxon class.
>
> NCBITaxon Class
>  * acronym
>  * common name
>  * equivalent name
>  * genetic code
>  * hidden
>  * left value
>  * mitogeneticcode
>  * noderank
>  * parent
>  * rightvalue
>  * scientific name
>  * synonym
>
This seems to invite inconsitent use. What is the difference between
> "equivalent name" and "synonym"?
> Similar to the BioPerl Taxonomy:Node, it has fields to store tree-like data
> (parent, rightvalue, etc.)
>
> An interesting question related to this taxonomy issue is how to compare
> them. When are taxonomies considered equal?
>
> --CZ
>
>
>
>
>


From czmasek at burnham.org  Thu May 28 19:49:05 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Thu, 28 May 2009 12:49:05 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
	<4A1D8965.5050404@burnham.org>
	<4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
Message-ID: <4A1EEAB1.2000402@burnham.org>

Hi, Diana
> What about treating "code" element as id, but with type "swiss-prot".

I think this would be acceptable.

Christian


From czmasek at burnham.org  Thu May 28 19:51:05 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Thu, 28 May 2009 12:51:05 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
	<4A1D8965.5050404@burnham.org>
	<4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
Message-ID: <4A1EEB29.3020508@burnham.org>

Hi, Diana
> What about treating "code" element as id, but with type "swiss-prot".

I think this would be acceptable.

Christian


From czmasek at burnham.org  Thu May 28 22:52:21 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Thu, 28 May 2009 15:52:21 -0700
Subject: [BioRuby] [Wg-phyloinformatics] bioruby classes for phyloxml
 support
In-Reply-To: <4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
References: <4057d3bf0905191407u44a10b9m656e615b2241bc14@mail.gmail.com>
	<EA2C8FBA-5231-4740-AB5E-209C244D9EC9@duke.edu>
	<D985B7C0-C151-4A95-8FDC-B3548439E08B@illinois.edu>
	<4A14D243.2010101@burnham.org>
	<86472996-C665-4AF0-A8A9-9E8D4EEB2A79@illinois.edu>
	<4057d3bf0905241729o69447925hd830404950fd28e1@mail.gmail.com>
	<4A1B18A8.1070104@burnham.org> <4A1B996E.2010702@ingm.it>
	<4057d3bf0905262002w448a7652leb48a40e680b13b8@mail.gmail.com>
	<4A1D8965.5050404@burnham.org>
	<4057d3bf0905271949x5b35bc87s17c681fb90d10294@mail.gmail.com>
Message-ID: <4A1F15A5.60801@burnham.org>

Hi, Diana:

Your wiki [at http://wiki.github.com/latvianlinuxgirl/bioruby] looks 
like a good idea!
I made some comments!

CZ



From rozziite at gmail.com  Sat May 30 21:27:52 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sat, 30 May 2009 17:27:52 -0400
Subject: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
Message-ID: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com>

Hi all,

So I looked more carefully at the sequence element of phyloXML and it
consists of information which cannot be mapped to Bio::Sequence object. I
suggest to have a sequence class which closely resembles phyloXML structure
and then have a method to extract relevant elements return Bio::Sequence
object.  What do you think?

Here on the left i listed phyloXML sequence tag elements and after the arrow
-> the possible corresponding attribute of Bio::Sequence
* type
** rna, dna  -> Bio::Sequence::NA -> molecule type
** aa -> Bio::Sequence::AA
* id_source (string ?) -> id_namespace
* id_ref (string ) -> entry_id
* symbol (string ?)
* accession
** source (example: "UniProtKB") ->
** id (example: "P17304") ->  primary_accession
* name (string )
* location (string ? )
* mol_seq (string) -> seq / Bio::Sequence::NA/AA
* uri
** desc (string)
** type (string )
** uri

* annotation []
** ref
** source
** evidence
** type
** desc
** confidence
** property []
** uri

* domain_architecture
** length
** domain []
*** from
*** to
*** confidence
*** id

Diana


From rozziite at gmail.com  Sun May 31 01:36:52 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sat, 30 May 2009 21:36:52 -0400
Subject: [BioRuby] Bioruby PhyloXML update
In-Reply-To: <4A1CEC2D.6010202@ingm.it>
References: <4057d3bf0905260517m32167f53j5ce8ca45b43ce655@mail.gmail.com> 
	<4A1CEC2D.6010202@ingm.it>
Message-ID: <4057d3bf0905301836k4cd0358btf87497b047a5f9d3@mail.gmail.com>

I looked at libxml-jruby and tried to install it, but i get "no such file to
load -- java" on the line "require 'java'". I have both jruby and java
installed. I also have .../jruby/bin directory in my $PATH.

Any suggestions?

Diana

On Wed, May 27, 2009 at 3:30 AM, Raoul JP Bonnal <bonnalraoul at ingm.it>wrote:

> Hi Diana,
> a portability issue.
> Have you guys verified if LibXML::XML is it running on JRuby ? I don't
> think so because it's implemented in C. A solution could be
> this http://github.com/mguterl/libxml-jruby/tree/master but today I can't
> access to it, probably due to my network problems.
>
> Some test, 1 year ago - last post -:
>
> http://www.nabble.com/comparing-xml-parsing-in-JRuby-and-MRI-td16268560.html#a16268560
>
> this is the test code - good portability example too - :
>
> https://svn.concord.org/svn/projects/trunk/common/ruby/xml_benchmarks/xml_benchmarks.rb
>
> Cheers.
>
> Diana Jaunzeikare ha scritto:
>
>> Hi all!
>>
>> Here is what was done during community bonding period:
>>
>>   - subscribed to mailing lists
>>   - created a blog <http://latvianlinuxgirl.blogspot.com/>
>>   - got familiar with Git (this was particularly useful:
>>   http://www.gitcasts.com/posts/railsconf-git-talk )
>>   - created GitHub account and forked bioruby project.
>>   - made first commit by adding sample phyloxml data files from
>>   www.phyloxml.org
>>   - reviewed BioPerl phyloXML implementation (also
>>   http://www.bioperl.org/wiki/HOWTO:Trees )
>>   - got familiar with libxml-ruby. Wrote simple program using both
>>   LibXML::XML::Reader and LibXML::XML::SAXParser to parse a simple xml
>> file.
>>   - reviewed Ruby classes - Bio:Tree, Bio::Pathways
>>   - After discussions in mailing lists it has been agreed to use
>>   LibXML-ruby library, the LibXML::XML::Reader class
>>
>>
>> This weeks plan:
>>
>>   - Start writing parser using LibXML::XML::Reader. It should return a
>>   Bio::Tree object.
>>   - Implement function next_tree to parse and return the next phylogeny.
>>   - Design Tree::Node object for containing phyloxml elements.
>>   - Start mapping phyloxml elements to Bio::Tree::Node, start with
>>   taxonomy, branch_length, scientific_name
>>   - Write simple unit tests.
>>
>>
>
>
>


From mail at michaelbarton.me.uk  Sun May 31 09:45:32 2009
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Sun, 31 May 2009 10:45:32 +0100
Subject: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
In-Reply-To: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com>
References: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com>
Message-ID: <c27b73c0905310245x198ebdb6p1f6a18d580c2e536@mail.gmail.com>

I'm not very familiar with phyloXML, but when you write sequence, do
you mean a multiple sequence alignment from which the phylogeny was
estimated? If that's the case, there is a MSA class in bioruby which
this could be mapped to perhaps?

2009/5/30 Diana Jaunzeikare <rozziite at gmail.com>:
> Hi all,
>
> So I looked more carefully at the sequence element of phyloXML and it
> consists of information which cannot be mapped to Bio::Sequence object. I
> suggest to have a sequence class which closely resembles phyloXML structure
> and then have a method to extract relevant elements return Bio::Sequence
> object. ?What do you think?
>
> Here on the left i listed phyloXML sequence tag elements and after the arrow
> -> the possible corresponding attribute of Bio::Sequence
> * type
> ** rna, dna ?-> Bio::Sequence::NA -> molecule type
> ** aa -> Bio::Sequence::AA
> * id_source (string ?) -> id_namespace
> * id_ref (string ) -> entry_id
> * symbol (string ?)
> * accession
> ** source (example: "UniProtKB") ->
> ** id (example: "P17304") -> ?primary_accession
> * name (string )
> * location (string ? )
> * mol_seq (string) -> seq / Bio::Sequence::NA/AA
> * uri
> ** desc (string)
> ** type (string )
> ** uri
>
> * annotation []
> ** ref
> ** source
> ** evidence
> ** type
> ** desc
> ** confidence
> ** property []
> ** uri
>
> * domain_architecture
> ** length
> ** domain []
> *** from
> *** to
> *** confidence
> *** id
>
> Diana
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



From czmasek at burnham.org  Sun May 31 17:17:49 2009
From: czmasek at burnham.org (Christian Zmasek)
Date: Sun, 31 May 2009 10:17:49 -0700
Subject: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
In-Reply-To: <c27b73c0905310245x198ebdb6p1f6a18d580c2e536@mail.gmail.com>
References: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com>,
	<c27b73c0905310245x198ebdb6p1f6a18d580c2e536@mail.gmail.com>
Message-ID: <E4F65F2E907A6F4B8582E0E44B2505EA1ADDE2A19F@MAIL07.burnham.org>

Hi, Michael:

Good point. Actually, it is not specified. It is just a sequence associated with a node. 
In my own work, I use it for the original sequence (before the introduction of gaps, and possible trimming of columns, during and after the alignment process).
Hence, I do not think reuse of the MSA class is appropriate.

Christian

 


________________________________________
From: bioruby-bounces at lists.open-bio.org [bioruby-bounces at lists.open-bio.org] On Behalf Of Michael Barton [mail at michaelbarton.me.uk]
Sent: Sunday, May 31, 2009 2:45 AM
To: Phyloinformatics Group; bioruby at lists.open-bio.org
Subject: Re: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence

I'm not very familiar with phyloXML, but when you write sequence, do
you mean a multiple sequence alignment from which the phylogeny was
estimated? If that's the case, there is a MSA class in bioruby which
this could be mapped to perhaps?

2009/5/30 Diana Jaunzeikare <rozziite at gmail.com>:
> Hi all,
>
> So I looked more carefully at the sequence element of phyloXML and it
> consists of information which cannot be mapped to Bio::Sequence object. I
> suggest to have a sequence class which closely resembles phyloXML structure
> and then have a method to extract relevant elements return Bio::Sequence
> object.  What do you think?
>
> Here on the left i listed phyloXML sequence tag elements and after the arrow
> -> the possible corresponding attribute of Bio::Sequence
> * type
> ** rna, dna  -> Bio::Sequence::NA -> molecule type
> ** aa -> Bio::Sequence::AA
> * id_source (string ?) -> id_namespace
> * id_ref (string ) -> entry_id
> * symbol (string ?)
> * accession
> ** source (example: "UniProtKB") ->
> ** id (example: "P17304") ->  primary_accession
> * name (string )
> * location (string ? )
> * mol_seq (string) -> seq / Bio::Sequence::NA/AA
> * uri
> ** desc (string)
> ** type (string )
> ** uri
>
> * annotation []
> ** ref
> ** source
> ** evidence
> ** type
> ** desc
> ** confidence
> ** property []
> ** uri
>
> * domain_architecture
> ** length
> ** domain []
> *** from
> *** to
> *** confidence
> *** id
>
> Diana
> _______________________________________________
> 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 mail at michaelbarton.me.uk  Sun May 31 20:59:09 2009
From: mail at michaelbarton.me.uk (Michael Barton)
Date: Sun, 31 May 2009 21:59:09 +0100
Subject: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
In-Reply-To: <E4F65F2E907A6F4B8582E0E44B2505EA1ADDE2A19F@MAIL07.burnham.org>
References: <4057d3bf0905301427u2e6cd6c8t759c29566b08f4db@mail.gmail.com> 
	<c27b73c0905310245x198ebdb6p1f6a18d580c2e536@mail.gmail.com> 
	<E4F65F2E907A6F4B8582E0E44B2505EA1ADDE2A19F@MAIL07.burnham.org>
Message-ID: <c27b73c0905311359q76ba2da2pae06fdcac6de9693@mail.gmail.com>

Hi Christian

Would this mean that there is a predicted single ancestor sequence
object associated at each node in a phylogenetic tree? You could start
at a specific node and traverse to ancestor or descendant nodes, and
therefore sequences? When you write original sequence, you mean the
multiple sequence alignment?

Cheers

Mike

2009/5/31 Christian Zmasek <czmasek at burnham.org>:
> Hi, Michael:
>
> Good point. Actually, it is not specified. It is just a sequence associated with a node.
> In my own work, I use it for the original sequence (before the introduction of gaps, and possible trimming of columns, during and after the alignment process).
> Hence, I do not think reuse of the MSA class is appropriate.
>
> Christian
>
>
>
>
> ________________________________________
> From: bioruby-bounces at lists.open-bio.org [bioruby-bounces at lists.open-bio.org] On Behalf Of Michael Barton [mail at michaelbarton.me.uk]
> Sent: Sunday, May 31, 2009 2:45 AM
> To: Phyloinformatics Group; bioruby at lists.open-bio.org
> Subject: Re: [BioRuby] GSOC: phyloXML for BioRuby: Mapping sequence
>
> I'm not very familiar with phyloXML, but when you write sequence, do
> you mean a multiple sequence alignment from which the phylogeny was
> estimated? If that's the case, there is a MSA class in bioruby which
> this could be mapped to perhaps?
>
> 2009/5/30 Diana Jaunzeikare <rozziite at gmail.com>:
>> Hi all,
>>
>> So I looked more carefully at the sequence element of phyloXML and it
>> consists of information which cannot be mapped to Bio::Sequence object. I
>> suggest to have a sequence class which closely resembles phyloXML structure
>> and then have a method to extract relevant elements return Bio::Sequence
>> object. ?What do you think?
>>
>> Here on the left i listed phyloXML sequence tag elements and after the arrow
>> -> the possible corresponding attribute of Bio::Sequence
>> * type
>> ** rna, dna ?-> Bio::Sequence::NA -> molecule type
>> ** aa -> Bio::Sequence::AA
>> * id_source (string ?) -> id_namespace
>> * id_ref (string ) -> entry_id
>> * symbol (string ?)
>> * accession
>> ** source (example: "UniProtKB") ->
>> ** id (example: "P17304") -> ?primary_accession
>> * name (string )
>> * location (string ? )
>> * mol_seq (string) -> seq / Bio::Sequence::NA/AA
>> * uri
>> ** desc (string)
>> ** type (string )
>> ** uri
>>
>> * annotation []
>> ** ref
>> ** source
>> ** evidence
>> ** type
>> ** desc
>> ** confidence
>> ** property []
>> ** uri
>>
>> * domain_architecture
>> ** length
>> ** domain []
>> *** from
>> *** to
>> *** confidence
>> *** id
>>
>> Diana
>> _______________________________________________
>> 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
>