From ngoto at gen-info.osaka-u.ac.jp  Tue Aug  4 08:03:31 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 4 Aug 2009 21:03:31 +0900
Subject: [BioRuby] how to convert sequence to fasta format with header
 information?
In-Reply-To: <4057d3bf0907301504i21d74c8dk6cccf6833476dcd6@mail.gmail.com>
References: <4057d3bf0907301504i21d74c8dk6cccf6833476dcd6@mail.gmail.com>
Message-ID: <20090804120333.198301CBC53D@idnmail.gen-info.osaka-u.ac.jp>

Hi,

It seems the document is wrong.

Bio::Sequence#to_fasta is deprecated, but Bio::Sequence::NA#to_fasta,
Bio::Sequence::AA#to_fasta, and Bio::Sequence::Generic#to_fasta
are NOT deprecated.

Currently, Bio::Sequence#output is defined, but no
Bio::Sequence::NA#output (and AA#output, Generic#output).

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

On Thu, 30 Jul 2009 18:04:59 -0400
Diana Jaunzeikare <rozziite at gmail.com> wrote:

> Hi all,
> 
> I want to retrieve sequence from a pdb file and save it in fasta format
> where* header holds the pdb entry id*. This is how I did it:
> 
> file = File.new('1OOP.pdb').gets(nil)
> structure = Bio::PDB.new(file)
> seq = structure.seqres['A']
> puts seq.to_fasta("1OOP", 70)
> 
> it works and produces result i want:
> 
> #>1OOP
> #GPPGEVMGRAIARVADTIGSGPVNSESIPALTAAETGHTSQVVPSDTMQTRHVKNYHSRSESTVENFLCR
> #SACVFYTTYENHDSDGDNFAYWVINTRQVAQLRRKLEMFTYARFDLELTFVITSTQEQPTVRGQDAPVLT
> #HQIMYVPPGGPVPTKVNSYSWQTSTNPSVFWTEGSAPPRMSVPFIGIGNAYSMFYDGWARFDKQGTYGIS
> #TLNNMGTLYMRHVNDGGPGPIVSTVRIYFKPKHVKTWVPRPPRLCQYQKAGNVNFEPTGVTEGRTDITTM
> #KTT
> 
> However, according to documation Bio::Sequence::Common#to_fasta is a
> deprecated method and it suggests to use Bio::Sequence#output, but when I
> modify code to
> 
> puts seq.output(:fasta)
> 
> it gives error that method is not defined. Also I don't see a way how to
> define the header.
> 
> What should i use in place of the deprecated to_fasta method?
> 
> Thanks,
> 
> Diana
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



From rozziite at gmail.com  Fri Aug  7 13:31:45 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Fri, 7 Aug 2009 13:31:45 -0400
Subject: [BioRuby] GSOC PhyloXML profiling, bottleneck is Bio::Tree#children
Message-ID: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com>

Hi all,

Here is update on Google Summer of Code Bioruby PhyloXML project. I was
profiling and refactoring Bioruby PhyloXML Parser code and got 67% speed
increase.

With profiling PhyloXML Writer the story is different. It takes 24minutes to
write the 1.5MB mollusca taxonomy tree and forever other larger files.
Again the bottleneck is bfs_shortest_path, which is called from
Tree#children method. It takes forever to just iterate over all the children
nodes.

To solve this I propose to save an array of the children of the node within
my PhyloXML::Node (which corresponds to a clade) class. This would also
ensure that when a phyloxml file is parsed and then written back, clades
would be the same order in the input and output files.


Have a good weekend,

Diana

From czmasek at burnham.org  Fri Aug  7 16:47:31 2009
From: czmasek at burnham.org (Christian Zmasek)
Date: Fri, 7 Aug 2009 13:47:31 -0700
Subject: [BioRuby] GSOC PhyloXML profiling,
	bottleneck is Bio::Tree#children
In-Reply-To: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com>
References: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com>
Message-ID: <E4F65F2E907A6F4B8582E0E44B2505EA326E0005B5@MAIL07.burnham.org>

Hi, Diana:

I think your array based solution is fine.

Although, at one point Bioruby's Tree might need to be enhanced, in order to avoid being slowed down by this bfs_shortest_path method. This issue is likely to prohibit (time-wise) many types of algorithms acting on large tree objects.

Christian


________________________________________
From: Diana Jaunzeikare [rozziite at gmail.com]
Sent: Friday, August 07, 2009 10:31 AM
To: Christian Zmasek; Phyloinformatics Group; Pjotr Prins; bioruby at lists.open-bio.org; Naohisa GOTO
Subject: GSOC PhyloXML profiling, bottleneck is Bio::Tree#children

Hi all,

Here is update on Google Summer of Code Bioruby PhyloXML project. I was profiling and refactoring Bioruby PhyloXML Parser code and got 67% speed increase.

With profiling PhyloXML Writer the story is different. It takes 24minutes to write the 1.5MB mollusca taxonomy tree and forever other larger files.  Again the bottleneck is bfs_shortest_path, which is called from Tree#children method. It takes forever to just iterate over all the children nodes.

To solve this I propose to save an array of the children of the node within my PhyloXML::Node (which corresponds to a clade) class. This would also ensure that when a phyloxml file is parsed and then written back, clades would be the same order in the input and output files.


Have a good weekend,

Diana


From ngoto at gen-info.osaka-u.ac.jp  Sun Aug  9 22:58:12 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 10 Aug 2009 11:58:12 +0900
Subject: [BioRuby] GSOC PhyloXML profiling,
	bottleneck is Bio::Tree#children
In-Reply-To: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com>
References: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com>
Message-ID: <20090810025814.9A8371CBC49D@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Fri, 7 Aug 2009 13:31:45 -0400
Diana Jaunzeikare <rozziite at gmail.com> wrote:

> Hi all,
> 
> Here is update on Google Summer of Code Bioruby PhyloXML project. I was
> profiling and refactoring Bioruby PhyloXML Parser code and got 67% speed
> increase.
> 
> With profiling PhyloXML Writer the story is different. It takes 24minutes to
> write the 1.5MB mollusca taxonomy tree and forever other larger files.
> Again the bottleneck is bfs_shortest_path, which is called from
> Tree#children method. It takes forever to just iterate over all the children
> nodes.

Bio::Tree uses graph algorithm  implemented in the Bio::Pathway class.
As you say, their implementations are naive and should be rewritten
in the future.

> To solve this I propose to save an array of the children of the node within
> my PhyloXML::Node (which corresponds to a clade) class. This would also
> ensure that when a phyloxml file is parsed and then written back, clades
> would be the same order in the input and output files.

How to maintain the array when modifying the tree, e.g. to add,
delete, or replace some nodes and edges?


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


> Have a good weekend,
> 
> Diana
> 

From rozziite at gmail.com  Mon Aug 10 11:00:54 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Mon, 10 Aug 2009 11:00:54 -0400
Subject: [BioRuby] GSOC PhyloXML profiling,
	bottleneck is Bio::Tree#children
In-Reply-To: <20090810025814.9A8371CBC49D@idnmail.gen-info.osaka-u.ac.jp>
References: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com> 
	<20090810025814.9A8371CBC49D@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <4057d3bf0908100800j544d0bcaqa063b0b9f5267a53@mail.gmail.com>

On Sun, Aug 9, 2009 at 10:58 PM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi,
>
> On Fri, 7 Aug 2009 13:31:45 -0400
> Diana Jaunzeikare <rozziite at gmail.com> wrote:
>
> > Hi all,
> >
> > Here is update on Google Summer of Code Bioruby PhyloXML project. I was
> > profiling and refactoring Bioruby PhyloXML Parser code and got 67% speed
> > increase.
> >
> > With profiling PhyloXML Writer the story is different. It takes 24minutes
> to
> > write the 1.5MB mollusca taxonomy tree and forever other larger files.
> > Again the bottleneck is bfs_shortest_path, which is called from
> > Tree#children method. It takes forever to just iterate over all the
> children
> > nodes.
>
> Bio::Tree uses graph algorithm  implemented in the Bio::Pathway class.
> As you say, their implementations are naive and should be rewritten
> in the future.
>
> > To solve this I propose to save an array of the children of the node
> within
> > my PhyloXML::Node (which corresponds to a clade) class. This would also
> > ensure that when a phyloxml file is parsed and then written back, clades
> > would be the same order in the input and output files.
>
> How to maintain the array when modifying the tree, e.g. to add,
> delete, or replace some nodes and edges?
>

I didn't think of this issue. I guess then instead of adding that support in
PhyloXML class I could rewrite Bio::Tree class, thus other projects based on
Bio::Tree class would benefit in the future.

Diana


>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
>
> > Have a good weekend,
> >
> > Diana
> >
>

From rozziite at gmail.com  Mon Aug 10 15:54:55 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Mon, 10 Aug 2009 15:54:55 -0400
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
Message-ID: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>

Hi all,

What was done last week:

* Coding. Added changes so that now it is completely compatible with
phyloxml schema 1.10

* Testing. added more unit tests (now writer has 9 tests, 26 assertions;
parser: 40 tests, 134 assertions)

* Profiling. I discovered that writer is really slow. The reason is the
implementation of the Tree#children method, which does bfs_shortest_path
algorithm. I had idea of tracking node children inside the node class as an
array, but Naohisa Goto pointed out that then I would also have to deal with
new node, edge addition, removal, etc. So better solution seems to, for now
leave it as it is, and first improve Bio::Tree class. I am planning to do
that after GSOC, since there is only one week left.

* Refactored parser class, got around 3-fold speed increase. Now it can
parse Metazoa taxonomy 33MB file in ~14 seconds (Ubuntu 9.04, ruby 1.8.7
[i486-linux], Intel Core 2 Duo P8600 @2.4GHz)

Next week:

* Create howto wiki page with code examples and usage.
* Do more testing (Anybody has some more phyloxml xml files for me to test,
other than those on phyloxml.org?)
* Any other suggestions from you?

Questions/issues:

* Where should the HOWTO and code example documentation go? Seems reasonable
for it to go here
 http://bioruby.open-bio.org/wiki/HOWTO:Trees and/or
http://bioruby.open-bio.org/wiki/Phyloxml_tree_format (which is linked from
previous link).

* How does integration to the master branch goes? Is all i have to do is
pull_request on github?

* I have implemented PhyloXML::Sequence#to_biosequence, however it returns
incomplete data, since info for Bio::Sequence#classification,
Bio::Sequence#species, Bio::Sequence#division would come from
PhyloXML::Taxonomy class, but it is not accessible from Sequence class.
Should there be PhyloXML::Node#to_biosequence method which would gather
information from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
Bio::Sequence should not hold taxonomic information?

You are all welcome to test my code. It is available on
http://github.com/latvianlinuxgirl/bioruby/tree/dev

Thanks,

Diana

From john.woods at marcottelab.org  Fri Aug  7 14:23:22 2009
From: john.woods at marcottelab.org (John O. Woods)
Date: Fri, 7 Aug 2009 13:23:22 -0500
Subject: [BioRuby] Feedback requested on OBO module
Message-ID: <91656c3f0908071123n3f130f29p2a1a33c4db50214d@mail.gmail.com>

Hi all,
I'm pretty new to Ruby (and Rails), first of all. I wrote a simple reader
for OBO files (attached). It does not write (currently), but it can
interface with ActiveRecord and acts-as-dag to create a directed acyclic
graph in a database.

As a newbie, I suspect I'm doing some things wrong, or at least not as
correctly as they could be done. For example, usually rails migrations that
fail undo all of their changes; but I can't figure out how I'd write that. I
attempted to do so, but it apparently does not work (have to set
:save_immediately => true to get it to work).

I'd love some feedback, if anyone would be willing to take a quick look at
my code.

I've also attached a test file from Flybase. An object can be created with:
od = Bio::OboDoc.new("filename.obo")

Thanks!
John

From ngoto at gen-info.osaka-u.ac.jp  Thu Aug 13 04:21:39 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 13 Aug 2009 17:21:39 +0900
Subject: [BioRuby] Feedback requested on OBO module
In-Reply-To: <91656c3f0908071123n3f130f29p2a1a33c4db50214d@mail.gmail.com>
References: <91656c3f0908071123n3f130f29p2a1a33c4db50214d@mail.gmail.com>
Message-ID: <20090813082140.0536D1CBC413@idnmail.gen-info.osaka-u.ac.jp>

Hi,

In this mailing list, attachment files are normally dropped.

To continue discussions, if the code is short, desribe it in the
message body. If it isn't short, put your code on your web site or
on a code repository (for example http://gist.github.com/ ) and
post only the URL.

Thanks.

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

On Fri, 7 Aug 2009 13:23:22 -0500
"John O. Woods" <john.woods at marcottelab.org> wrote:

> Hi all,
> I'm pretty new to Ruby (and Rails), first of all. I wrote a simple reader
> for OBO files (attached). It does not write (currently), but it can
> interface with ActiveRecord and acts-as-dag to create a directed acyclic
> graph in a database.
> 
> As a newbie, I suspect I'm doing some things wrong, or at least not as
> correctly as they could be done. For example, usually rails migrations that
> fail undo all of their changes; but I can't figure out how I'd write that. I
> attempted to do so, but it apparently does not work (have to set
> :save_immediately => true to get it to work).
> 
> I'd love some feedback, if anyone would be willing to take a quick look at
> my code.
> 
> I've also attached a test file from Flybase. An object can be created with:
> od = Bio::OboDoc.new("filename.obo")
> 
> Thanks!
> John
> 


From rozziite at gmail.com  Thu Aug 13 17:50:01 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Thu, 13 Aug 2009 17:50:01 -0400
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
Message-ID: <4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>

Hi all,

I added here a HOWTO for BioRuby PhyloXML implementation

https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation

Let me know, what you think

Diana

On Mon, Aug 10, 2009 at 3:54 PM, Diana Jaunzeikare <rozziite at gmail.com>wrote:

> Hi all,
>
> What was done last week:
>
> * Coding. Added changes so that now it is completely compatible with
> phyloxml schema 1.10
>
> * Testing. added more unit tests (now writer has 9 tests, 26 assertions;
> parser: 40 tests, 134 assertions)
>
> * Profiling. I discovered that writer is really slow. The reason is the
> implementation of the Tree#children method, which does bfs_shortest_path
> algorithm. I had idea of tracking node children inside the node class as an
> array, but Naohisa Goto pointed out that then I would also have to deal with
> new node, edge addition, removal, etc. So better solution seems to, for now
> leave it as it is, and first improve Bio::Tree class. I am planning to do
> that after GSOC, since there is only one week left.
>
> * Refactored parser class, got around 3-fold speed increase. Now it can
> parse Metazoa taxonomy 33MB file in ~14 seconds (Ubuntu 9.04, ruby 1.8.7
> [i486-linux], Intel Core 2 Duo P8600 @2.4GHz)
>
> Next week:
>
> * Create howto wiki page with code examples and usage.
> * Do more testing (Anybody has some more phyloxml xml files for me to test,
> other than those on phyloxml.org?)
> * Any other suggestions from you?
>
> Questions/issues:
>
> * Where should the HOWTO and code example documentation go? Seems
> reasonable for it to go here
>  http://bioruby.open-bio.org/wiki/HOWTO:Trees and/or
> http://bioruby.open-bio.org/wiki/Phyloxml_tree_format (which is linked
> from previous link).
>
> * How does integration to the master branch goes? Is all i have to do is
> pull_request on github?
>
> * I have implemented PhyloXML::Sequence#to_biosequence, however it returns
> incomplete data, since info for Bio::Sequence#classification,
> Bio::Sequence#species, Bio::Sequence#division would come from
> PhyloXML::Taxonomy class, but it is not accessible from Sequence class.
> Should there be PhyloXML::Node#to_biosequence method which would gather
> information from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
> Bio::Sequence should not hold taxonomic information?
>
> You are all welcome to test my code. It is available on
> http://github.com/latvianlinuxgirl/bioruby/tree/dev
>
> Thanks,
>
> Diana
>

From czmasek at burnham.org  Fri Aug 14 14:41:13 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Fri, 14 Aug 2009 11:41:13 -0700
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
	<4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
Message-ID: <4A85AFC9.4020106@burnham.org>

Very nice!!

I guess this will be placed/copied to the BioRuby tutorial (at 
http://bioruby.open-bio.org/wiki/Tutorial) at one point, correct?



A very tiny, minuscule even, issue I noticed (and maybe even a problem 
of my web browser):

A the very end, the blue box seems broken at the "wrong place" -- so to 
speak, i.e.

"#Once we know whats there, lets output just sequences
phyloxml.other[0].children.each do |node|
   puts node.value
end"

and

"#=>
#
#acgtcgcggcccgtggaagtcctctcct
#aggtcgcggcctgtggaagtcctctcct
#taaatcgc--cccgtgg-agtccc-cct"

should be in the same box, but they appear to be in different ones.

Christian





Diana Jaunzeikare wrote:
> Hi all,
> 
> I added here a HOWTO for BioRuby PhyloXML implementation
> 
> https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
> 
> Let me know, what you think
> 
> Diana
> 
> On Mon, Aug 10, 2009 at 3:54 PM, Diana Jaunzeikare <rozziite at gmail.com 
> <mailto:rozziite at gmail.com>> wrote:
> 
>     Hi all,
> 
>     What was done last week:
> 
>     * Coding. Added changes so that now it is completely compatible with
>     phyloxml schema 1.10
> 
>     * Testing. added more unit tests (now writer has 9 tests, 26
>     assertions; parser: 40 tests, 134 assertions)
> 
>     * Profiling. I discovered that writer is really slow. The reason is
>     the implementation of the Tree#children method, which does
>     bfs_shortest_path algorithm. I had idea of tracking node children
>     inside the node class as an array, but Naohisa Goto pointed out that
>     then I would also have to deal with new node, edge addition,
>     removal, etc. So better solution seems to, for now leave it as it
>     is, and first improve Bio::Tree class. I am planning to do that
>     after GSOC, since there is only one week left.
> 
>     * Refactored parser class, got around 3-fold speed increase. Now it
>     can parse Metazoa taxonomy 33MB file in ~14 seconds (Ubuntu 9.04,
>     ruby 1.8.7 [i486-linux], Intel Core 2 Duo P8600 @2.4GHz)
> 
>     Next week:
> 
>     * Create howto wiki page with code examples and usage.
>     * Do more testing (Anybody has some more phyloxml xml files for me
>     to test, other than those on phyloxml.org <http://phyloxml.org>?)
>     * Any other suggestions from you?
> 
>     Questions/issues:
> 
>     * Where should the HOWTO and code example documentation go? Seems
>     reasonable for it to go here
>      http://bioruby.open-bio.org/wiki/HOWTO:Trees and/or
>     http://bioruby.open-bio.org/wiki/Phyloxml_tree_format (which is
>     linked from previous link).
> 
>     * How does integration to the master branch goes? Is all i have to
>     do is pull_request on github?
> 
>     * I have implemented PhyloXML::Sequence#to_biosequence, however it
>     returns incomplete data, since info for
>     Bio::Sequence#classification, Bio::Sequence#species,
>     Bio::Sequence#division would come from PhyloXML::Taxonomy class, but
>     it is not accessible from Sequence class. Should there be
>     PhyloXML::Node#to_biosequence method which would gather information
>     from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
>     Bio::Sequence should not hold taxonomic information?
> 
>     You are all welcome to test my code. It is available on
>     http://github.com/latvianlinuxgirl/bioruby/tree/dev
> 
>     Thanks,
> 
>     Diana
> 
> 


From czmasek at burnham.org  Fri Aug 14 14:52:04 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Fri, 14 Aug 2009 11:52:04 -0700
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
	<4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
Message-ID: <4A85B254.8020601@burnham.org>

Hi, Diana:

> 
>     * How does integration to the master branch goes? Is all i have to
>     do is pull_request on github?

I think so (never done this myself, though). Maybe the git experts can 
answer this?


>     * I have implemented PhyloXML::Sequence#to_biosequence, however it
>     returns incomplete data, since info for
>     Bio::Sequence#classification, Bio::Sequence#species,
>     Bio::Sequence#division would come from PhyloXML::Taxonomy class, but
>     it is not accessible from Sequence class. Should there be
>     PhyloXML::Node#to_biosequence method which would gather information
>     from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
>     Bio::Sequence should not hold taxonomic information?

Good point. Personally, I would leave your 
PhyloXML::Sequence#to_biosequence as it is (and add a warning about this 
  to the documentation) and, in addition, create 
PhyloXML::Node#to_biosequence -- although, I would not call it 
to_biosequence but maybe something like extract_biosequence.
Needless to say, that an almost infinite number of "solutions" to this 
exists, without a clear "winner" (in my opinion).

Christian


From ngoto at gen-info.osaka-u.ac.jp  Sat Aug 15 06:38:24 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 15 Aug 2009 19:38:24 +0900
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4A85B254.8020601@burnham.org>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
	<4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
	<4A85B254.8020601@burnham.org>
Message-ID: <20090815103824.DEC901CBC494@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Fri, 14 Aug 2009 11:52:04 -0700
Christian M Zmasek <czmasek at burnham.org> wrote:

> Hi, Diana:
> 
> > 
> >     * How does integration to the master branch goes? Is all i have to
> >     do is pull_request on github?
> 
> I think so (never done this myself, though). Maybe the git experts can 
> answer this?

I'll soon release 1.3.1, bug-fix release of 1.3.0.
After that, the PhyloXML support and some other new functions
such as Chromatogram class http://github.com/aunderwo/bioruby/tree
will be merged, and will be released as 1.4.0.

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

From andrew.j.grimm at gmail.com  Sun Aug 16 06:42:23 2009
From: andrew.j.grimm at gmail.com (Andrew Grimm)
Date: Sun, 16 Aug 2009 20:42:23 +1000
Subject: [BioRuby] Code style question
Message-ID: <b9140daa0908160342s7d12abebk94c4ab1303f212ee@mail.gmail.com>

The Readme for developers mentions that

  if __FILE__ == $0

is deprecated for testing.

In lib/bio/db/fasta.rb , there's a __FILE__ == $0 that isn't used for
testing, but for demonstrating what the module's supposed to do. Is
this kind of coding non-deprecated?

Andrew

From ngoto at gen-info.osaka-u.ac.jp  Sun Aug 16 08:57:10 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto)
Date: Sun, 16 Aug 2009 21:57:10 +0900
Subject: [BioRuby] Code style question
In-Reply-To: <b9140daa0908160342s7d12abebk94c4ab1303f212ee@mail.gmail.com>
References: <b9140daa0908160342s7d12abebk94c4ab1303f212ee@mail.gmail.com>
Message-ID: <20090816215623.4B48.EEF6E030@gen-info.osaka-u.ac.jp>

Hi,

> The Readme for developers mentions that
> 
>   if __FILE__ == $0
> 
> is deprecated for testing.
> 
> In lib/bio/db/fasta.rb , there's a __FILE__ == $0 that isn't used for
> testing, but for demonstrating what the module's supposed to do. Is
> this kind of coding non-deprecated?
> 
> Andrew

Yes, deprecated for new codes. 

Old codes before the style have been deprecated may be existed.
We gradually move and rewrite them to unit tests and/or sample codes.

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



From rozziite at gmail.com  Sun Aug 16 16:09:49 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sun, 16 Aug 2009 16:09:49 -0400
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4A85B254.8020601@burnham.org>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com> 
	<4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com> 
	<4A85B254.8020601@burnham.org>
Message-ID: <4057d3bf0908161309p634fd95bt24b81debe9b2a669@mail.gmail.com>

On Fri, Aug 14, 2009 at 2:52 PM, Christian M Zmasek <czmasek at burnham.org>wrote:

> Hi, Diana:
>
>
>>    * How does integration to the master branch goes? Is all i have to
>>    do is pull_request on github?
>>
>
> I think so (never done this myself, though). Maybe the git experts can
> answer this?
>
>
>     * I have implemented PhyloXML::Sequence#to_biosequence, however it
>>    returns incomplete data, since info for
>>    Bio::Sequence#classification, Bio::Sequence#species,
>>    Bio::Sequence#division would come from PhyloXML::Taxonomy class, but
>>    it is not accessible from Sequence class. Should there be
>>    PhyloXML::Node#to_biosequence method which would gather information
>>    from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
>>    Bio::Sequence should not hold taxonomic information?
>>
>
> Good point. Personally, I would leave your
> PhyloXML::Sequence#to_biosequence as it is (and add a warning about this  to
> the documentation) and, in addition, create PhyloXML::Node#to_biosequence --
> although, I would not call it to_biosequence but maybe something like
> extract_biosequence.
> Needless to say, that an almost infinite number of "solutions" to this
> exists, without a clear "winner" (in my opinion).
>
> Christian
>
>
I added PhyloXML::Node#extract_biosequence method. It first calls
sequence#to_biosequence and then adds additional information from taxonomy
elements.

Diana

From czmasek at burnham.org  Sun Aug 16 21:57:06 2009
From: czmasek at burnham.org (Christian Zmasek)
Date: Sun, 16 Aug 2009 18:57:06 -0700
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4057d3bf0908161309p634fd95bt24b81debe9b2a669@mail.gmail.com>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
	<4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
	<4A85B254.8020601@burnham.org>,
	<4057d3bf0908161309p634fd95bt24b81debe9b2a669@mail.gmail.com>
Message-ID: <E4F65F2E907A6F4B8582E0E44B2505EA32FBA3456A@MAIL07.burnham.org>

Sounds very good!

________________________________________
From: Diana Jaunzeikare [rozziite at gmail.com]
Sent: Sunday, August 16, 2009 1:09 PM
To: Christian Zmasek
Cc: bioruby at lists.open-bio.org; Pjotr Prins; Naohisa GOTO; Phyloinformatics Group
Subject: Re: GSOC: Bioruby PhyloXML update 12

On Fri, Aug 14, 2009 at 2:52 PM, Christian M Zmasek <czmasek at burnham.org<mailto:czmasek at burnham.org>> wrote:
Hi, Diana:



   * How does integration to the master branch goes? Is all i have to
   do is pull_request on github?

I think so (never done this myself, though). Maybe the git experts can answer this?



   * I have implemented PhyloXML::Sequence#to_biosequence, however it
   returns incomplete data, since info for
   Bio::Sequence#classification, Bio::Sequence#species,
   Bio::Sequence#division would come from PhyloXML::Taxonomy class, but
   it is not accessible from Sequence class. Should there be
   PhyloXML::Node#to_biosequence method which would gather information
   from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
   Bio::Sequence should not hold taxonomic information?

Good point. Personally, I would leave your PhyloXML::Sequence#to_biosequence as it is (and add a warning about this  to the documentation) and, in addition, create PhyloXML::Node#to_biosequence -- although, I would not call it to_biosequence but maybe something like extract_biosequence.
Needless to say, that an almost infinite number of "solutions" to this exists, without a clear "winner" (in my opinion).

Christian


I added PhyloXML::Node#extract_biosequence method. It first calls sequence#to_biosequence and then adds additional information from taxonomy elements.

Diana



From rozziite at gmail.com  Mon Aug 17 11:20:45 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Mon, 17 Aug 2009 11:20:45 -0400
Subject: [BioRuby] Bioruby PhyloXML pencils down
Message-ID: <4057d3bf0908170820g552389d7r958a52af3f62b7d5@mail.gmail.com>

Hi all,

So the Google Summer of Code is over. I had a great time learning and
improving my programming skills in real world environment. Especially I am
glad that I learned more of "doing things in the ruby way".  I think that
writing open source will definitely help me to land with a better job after
graduation since the result is something i can actually show to the
potential employers as example of my work.

Here is the summary:

* Wrote Bio::PhyloXML::Parser class which is responsible for parsing xml
files in phyloxml format. It inherits from Bio::Tree and thus have all the
functionality Bio::Tree class have.

* Wrote Bio::PhyloXML::Writer class which is responsible for writing
(hopefully) valid xml files against phyloxml schema. For most part it
produces xml files that validate against phyloxml schema, but probably it is
possible to produce artificial example when it is not, since not everywhere
i have checks for valid input or data type. This is where i can improve in
future.

* Since these classes are meant to deal with big data files, I changed code
several times to make it faster. I managed to improve the speed of the
Parser by a lot, but not for the Writer. In order to improve speed of the
Writer, i will first improve the underlying Bio::Tree class (thus others
also might benefit from faster Bio::Tree class).

* Bio::PhyloXML module holds classes corresponding to complex phyloxml
elements. Here http://wiki.github.com/latvianlinuxgirl/bioruby is the design
of classes.

* The code is here http://github.com/latvianlinuxgirl/bioruby/tree/dev

* The project page is here:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby,
where probably I will continue to post future plan.

* Code examples are
https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation.
The same information is also incorporated in bioruby tutorial.


I will definitely stay involved in BioRuby and open source community. The
next step will be to improve Bio::Tree class, especially Bio::Tree#parent
and Bio::Tree#children methods. Next semester I will be taking Algorithms
class, so maybe I will be able to apply that knowledge to this task.  And of
course I plan to maintain my code, since when people will start using the
code, bugs will start to creep up.

I would like to thank my mentors Christian and Pjotr for support and timely
answers to my questions. Also thanks to Naohisa and others who answered my
questions and helped me.

Diana

From john.woods at marcottelab.org  Fri Aug 21 20:04:03 2009
From: john.woods at marcottelab.org (John O. Woods)
Date: Fri, 21 Aug 2009 19:04:03 -0500
Subject: [BioRuby] Batch Entrez search
Message-ID: <91656c3f0908211704p5b97f909ve168f4fcb7873fee@mail.gmail.com>

Right now I'm doing, one at a time: n.search("gene", "FBgn0041721")I'm
trying to get the gene ID corresponding to a Flybase gene ID.

This takes forever, since you can only do one every three seconds.

Also, sometimes it returns two items, and one might be deprecated--but
there's no way to tell.

Is there a way to batch search with BioRuby for a whole bunch of Flybase
IDs?

Many thanks,
John

Marcotte Lab | The University of Texas at Austin

From tomoakin at kenroku.kanazawa-u.ac.jp  Sun Aug 23 22:21:18 2009
From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA)
Date: Mon, 24 Aug 2009 11:21:18 +0900
Subject: [BioRuby] Batch Entrez search
In-Reply-To: <91656c3f0908211704p5b97f909ve168f4fcb7873fee@mail.gmail.com>
References: <91656c3f0908211704p5b97f909ve168f4fcb7873fee@mail.gmail.com>
Message-ID: <AB3385C8-0DE1-4F42-8532-CA128EA2B140@kenroku.kanazawa-u.ac.jp>

Hi,

> Is there a way to batch search with BioRuby for a whole bunch of  
> Flybase
> IDs?


According to
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpgene&part=genefaq
the data for entrez gene are available in
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

If you need really a lot, perhaps its better to download that file  
(about 93 Mbytes).
(It contains data for other organisms, which is not necessary, but  
does not take forever)
The format seems simple enough that you can easily get the gene ID  
for a flybase ID.

#Format: tax_id GeneID Symbol LocusTag Synonyms dbXrefs chromosome  
map_location description type_of_gene  
Symbol_from_nomenclature_authority Full_name_from_nomenclatur
e_authority Nomenclature_status Other_designations Modification_date  
(tab is used as a separator, pound sign - start of a comment)

-- 
Tomoaki NISHIYAMA

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


From marc.hoeppner at molbio.su.se  Mon Aug 24 01:36:48 2009
From: marc.hoeppner at molbio.su.se (Marc Hoeppner)
Date: Mon, 24 Aug 2009 07:36:48 +0200
Subject: [BioRuby] Batch Entrez search
In-Reply-To: <AB3385C8-0DE1-4F42-8532-CA128EA2B140@kenroku.kanazawa-u.ac.jp>
References: <91656c3f0908211704p5b97f909ve168f4fcb7873fee@mail.gmail.com>
	<AB3385C8-0DE1-4F42-8532-CA128EA2B140@kenroku.kanazawa-u.ac.jp>
Message-ID: <4A9226F0.4050206@molbio.su.se>

Hi,

I suppose for FlyBase genes you could also use the ruby Ensembl API.

Something like:

require 'ensembl'


Ensembl::Core::DBConnection('drosophila_melanogaster','55)

IO.foreach('my_infile') do |flybase_id|

    gene = Ensembl::Core::Gene.find_by_stable_id(flybase_id)
   
    gene.all_xrefs.each do |xref|
      
        puts xref
   
    end

end

Well, you get the idea. The methods are well documented in the 
corresponding API, but when in doubt I can offer some help, too.

P.S.: To make it real easy you could also use the BioMart on 
www.ensembl.org - unless you need this to be a script.

Cheers,

Marc
> Hi,
>
>> Is there a way to batch search with BioRuby for a whole bunch of Flybase
>> IDs?
>
>
> According to
> http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpgene&part=genefaq
> the data for entrez gene are available in
> ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
>
> If you need really a lot, perhaps its better to download that file 
> (about 93 Mbytes).
> (It contains data for other organisms, which is not necessary, but 
> does not take forever)
> The format seems simple enough that you can easily get the gene ID for 
> a flybase ID.
>
> #Format: tax_id GeneID Symbol LocusTag Synonyms dbXrefs chromosome 
> map_location description type_of_gene 
> Symbol_from_nomenclature_authority Full_name_from_nomenclatur
> e_authority Nomenclature_status Other_designations Modification_date 
> (tab is used as a separator, pound sign - start of a comment)
>


-- 

Marc P. Hoeppner
PhD student
Department of Molecular Biology and Functional Genomics
Stockholm University, 10691 Stockholm, Sweden

marc.hoeppner at molbio.su.se
Tel: +46 (0)8 - 164195


From john.woods at marcottelab.org  Mon Aug 24 08:44:31 2009
From: john.woods at marcottelab.org (John O. Woods)
Date: Mon, 24 Aug 2009 07:44:31 -0500
Subject: [BioRuby] Batch Entrez search
In-Reply-To: <4A9226F0.4050206@molbio.su.se>
References: <91656c3f0908211704p5b97f909ve168f4fcb7873fee@mail.gmail.com>
	<AB3385C8-0DE1-4F42-8532-CA128EA2B140@kenroku.kanazawa-u.ac.jp>
	<4A9226F0.4050206@molbio.su.se>
Message-ID: <91656c3f0908240544h20577825n38817c7667081b90@mail.gmail.com>

Unfortunately, many Flybase IDs seem to be missing from BioMart, which leads
me to think they'd also be absent from Ensembl.

On Mon, Aug 24, 2009 at 12:36 AM, Marc Hoeppner
<marc.hoeppner at molbio.su.se>wrote:

> Hi,
>
> I suppose for FlyBase genes you could also use the ruby Ensembl API.
>
> Something like:
>
> require 'ensembl'
>
>
> Ensembl::Core::DBConnection('drosophila_melanogaster','55)
>
> IO.foreach('my_infile') do |flybase_id|
>
>   gene = Ensembl::Core::Gene.find_by_stable_id(flybase_id)
>     gene.all_xrefs.each do |xref|
>           puts xref
>     end
>
> end
>
> Well, you get the idea. The methods are well documented in the
> corresponding API, but when in doubt I can offer some help, too.
>
> P.S.: To make it real easy you could also use the BioMart on
> www.ensembl.org - unless you need this to be a script.
>
> Cheers,
>
> Marc
>
>> Hi,
>>
>>  Is there a way to batch search with BioRuby for a whole bunch of Flybase
>>> IDs?
>>>
>>
>>
>> According to
>> http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpgene&part=genefaq
>> the data for entrez gene are available in
>> ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
>>
>> If you need really a lot, perhaps its better to download that file (about
>> 93 Mbytes).
>> (It contains data for other organisms, which is not necessary, but does
>> not take forever)
>> The format seems simple enough that you can easily get the gene ID for a
>> flybase ID.
>>
>> #Format: tax_id GeneID Symbol LocusTag Synonyms dbXrefs chromosome
>> map_location description type_of_gene Symbol_from_nomenclature_authority
>> Full_name_from_nomenclatur
>> e_authority Nomenclature_status Other_designations Modification_date (tab
>> is used as a separator, pound sign - start of a comment)
>>
>>
>
> --
>
> Marc P. Hoeppner
> PhD student
> Department of Molecular Biology and Functional Genomics
> Stockholm University, 10691 Stockholm, Sweden
>
> marc.hoeppner at molbio.su.se
> Tel: +46 (0)8 - 164195
>
>

From biopython at maubp.freeserve.co.uk  Thu Aug 27 06:46:17 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 27 Aug 2009 11:46:17 +0100
Subject: [BioRuby] FASTQ in BioRuby?
Message-ID: <320fb6e00908270346y5d653d29mdd2dc7ebc76af3c1@mail.gmail.com>

Hello BioRuby team,

I am one of the Biopython developers, and together with Peter Rice
(EMBOSS) and Chris Fields (BioPerl) we have been coordinating
how these Open Bioinformatics Foundation (OBF) projects will
interpret the FASTQ file format used in next generation sequencing.

This includes standardising our naming conventions for the original
Sanger FASTQ variant, and the later Solexa/early Illumina, and
recent Illumina 1.3+ variants. We have also put together a set of
test files, including reference conversions between the different
FASTQ variants.

We would be delighted to get BioRuby involved. I tried to contact
Naohisa Goto about this directly last month, but perhaps my email
did not arrive. If BioRuby is working on (or planning to work on)
FASTQ support, please could the developers concerned sign up
to the OBF joint mailing list where we have been discussing this:
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thank you,

Peter

From ngoto at gen-info.osaka-u.ac.jp  Thu Aug 27 07:20:46 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 27 Aug 2009 20:20:46 +0900
Subject: [BioRuby] [Open-bio-l] FASTQ in BioRuby?
In-Reply-To: <320fb6e00908270346y5d653d29mdd2dc7ebc76af3c1@mail.gmail.com>
References: <320fb6e00908270346y5d653d29mdd2dc7ebc76af3c1@mail.gmail.com>
Message-ID: <20090827112046.E2C741CBC4BA@idnmail.gen-info.osaka-u.ac.jp>

Hello Peter,

sorry for responding too late. I've subscribed to open-bio-l,
but I could not actively join to the discussions, because of
lack of my knowledge about FASTQ.

There is a small primitive code attempt to support FASTQ format
in BioRuby, which is not yet merged in the main repository.
http://github.com/ngoto/bioruby/tree/master

Recently, Anthony Underwood contributed chromatgram classes
to support SCF/ABI formats, which will be merged soon,
after bug-fix maintenance release of 1.3.1.
http://github.com/aunderwo/bioruby/tree/master

I'm now planning to rewrite my FASTQ code to be consistent
with the chromatgram classes, and with the open-bio standards.

Thank you,

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

On Thu, 27 Aug 2009 11:46:17 +0100
Peter <biopython at maubp.freeserve.co.uk> wrote:

> Hello BioRuby team,
> 
> I am one of the Biopython developers, and together with Peter Rice
> (EMBOSS) and Chris Fields (BioPerl) we have been coordinating
> how these Open Bioinformatics Foundation (OBF) projects will
> interpret the FASTQ file format used in next generation sequencing.
> 
> This includes standardising our naming conventions for the original
> Sanger FASTQ variant, and the later Solexa/early Illumina, and
> recent Illumina 1.3+ variants. We have also put together a set of
> test files, including reference conversions between the different
> FASTQ variants.
> 
> We would be delighted to get BioRuby involved. I tried to contact
> Naohisa Goto about this directly last month, but perhaps my email
> did not arrive. If BioRuby is working on (or planning to work on)
> FASTQ support, please could the developers concerned sign up
> to the OBF joint mailing list where we have been discussing this:
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> Thank you,
> 
> Peter
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l


From biopython at maubp.freeserve.co.uk  Thu Aug 27 08:08:28 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 27 Aug 2009 13:08:28 +0100
Subject: [BioRuby] [Open-bio-l] FASTQ in BioRuby?
In-Reply-To: <20090827112046.E2C741CBC4BA@idnmail.gen-info.osaka-u.ac.jp>
References: <320fb6e00908270346y5d653d29mdd2dc7ebc76af3c1@mail.gmail.com>
	<20090827112046.E2C741CBC4BA@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <320fb6e00908270508o485ba990k96b8bd3b722c09b6@mail.gmail.com>

On Thu, Aug 27, 2009 at 12:20 PM, Naohisa
GOTO<ngoto at gen-info.osaka-u.ac.jp> wrote:
>
> Hello Peter,
>
> sorry for responding too late. I've subscribed to open-bio-l,
> but I could not actively join to the discussions, because of
> lack of my knowledge about FASTQ.
>
> There is a small primitive code attempt to support FASTQ format
> in BioRuby, which is not yet merged in the main repository.
> http://github.com/ngoto/bioruby/tree/master
>
> Recently, Anthony Underwood contributed chromatgram classes
> to support SCF/ABI formats, which will be merged soon,
> after bug-fix maintenance release of 1.3.1.
> http://github.com/aunderwo/bioruby/tree/master
>
> I'm now planning to rewrite my FASTQ code to be consistent
> with the chromatgram classes, and with the open-bio standards.
>
> Thank you,
>
> Naohisa Goto

That is excellent news :)

I'm not sure how format names work in BioRuby, but if you
do have a set of format names as strings as we do in
Biopython, BioPerl and EMBOSS it would be nice to be
consistent here:

http://biopython.org/wiki/SeqIO
http://bioperl.org/wiki/HOWTO:SeqIO
http://emboss.sourceforge.net/docs/themes/SequenceFormats.html

There is some basic information on wikipedia, but this
does not go into detail:
http://www.bioperl.org/wiki/FASTQ_sequence_format

Please feel free to ask any questions about how we are
interpreting things.

Thank you,

Peter

From ngoto at gen-info.osaka-u.ac.jp  Mon Aug 31 10:22:11 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 31 Aug 2009 23:22:11 +0900
Subject: [BioRuby] SIM4 parser
In-Reply-To: <0C3F8576-899A-426E-869A-C9DCF8F47868@kenroku.kanazawa-u.ac.jp>
References: <5510B566-E723-4AEE-8DEC-63BE1ABD9F19@kenroku.kanazawa-u.ac.jp>
	<0C3F8576-899A-426E-869A-C9DCF8F47868@kenroku.kanazawa-u.ac.jp>
Message-ID: <20090831142212.3468E1CBC58D@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Sun, 5 Jul 2009 20:28:33 +0900
Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp> wrote:

> Hi,
> 
> > A way to resolve may to check if the start address match the  
> > address that
> > was specified in the previous section stating the ranges of the  
> > matches.
> > I'm considering implementing this way.
> 
> 
> A working code is obtained and a diff relative to 1.3.0 is attached.
> The code was changed to parse alignment only after the SegemntPairs
> are prepared

The bug is fixed.
http://github.com/bioruby/bioruby/commit/02d531e36ecf789f232cf3e05f85391b60279f00

Thank you for sending a patch. I didn't fully use your patch,
but it was very helpful.

> During this work, I also noticed that the semantics of the structure
> might be misunderstood:
> 1. The mark after the match, either "->", "<-", "--", or "=="
> does not represent the direction of the exon, but indicates
>   the presumed direction of the intron following the exon.
> "--" corresponds in case part of the intervening sequence
> and midline is shown and
> "==" is for cases without information for intervening sequence.
> I do not understand how these patterns are determined by SIM4,
> but "->" and "<-" can be estimated based on GU-AG rule.
> Since these directions are essentially assigned to the
> introns rather than exons, it might be inappropriate to assign
> these strings to the exon.  There is actually rare cases that
> introns in different direction is deduced: in such case
> assuming the direction of the exon is same as the 3' intron
> rather than 5' intron of the exon is not desired.  So, it seems
> arguable to make directions for exon deprecated.
>
>  From current state of the parser, I bet there are few people using
> bioruby to parse sim4 alignment output, and changing the interface
> is acceptable this time.

You are right. However, currently, to keep compatibility,
the method Bio::Sim4::Report::SegmentPair#direction is still
being used.  In next major release (1.4.0?), the method will
be deprecated, and other method would be added.

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

From ngoto at gen-info.osaka-u.ac.jp  Tue Aug  4 12:03:31 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Tue, 4 Aug 2009 21:03:31 +0900
Subject: [BioRuby] how to convert sequence to fasta format with header
 information?
In-Reply-To: <4057d3bf0907301504i21d74c8dk6cccf6833476dcd6@mail.gmail.com>
References: <4057d3bf0907301504i21d74c8dk6cccf6833476dcd6@mail.gmail.com>
Message-ID: <20090804120333.198301CBC53D@idnmail.gen-info.osaka-u.ac.jp>

Hi,

It seems the document is wrong.

Bio::Sequence#to_fasta is deprecated, but Bio::Sequence::NA#to_fasta,
Bio::Sequence::AA#to_fasta, and Bio::Sequence::Generic#to_fasta
are NOT deprecated.

Currently, Bio::Sequence#output is defined, but no
Bio::Sequence::NA#output (and AA#output, Generic#output).

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

On Thu, 30 Jul 2009 18:04:59 -0400
Diana Jaunzeikare <rozziite at gmail.com> wrote:

> Hi all,
> 
> I want to retrieve sequence from a pdb file and save it in fasta format
> where* header holds the pdb entry id*. This is how I did it:
> 
> file = File.new('1OOP.pdb').gets(nil)
> structure = Bio::PDB.new(file)
> seq = structure.seqres['A']
> puts seq.to_fasta("1OOP", 70)
> 
> it works and produces result i want:
> 
> #>1OOP
> #GPPGEVMGRAIARVADTIGSGPVNSESIPALTAAETGHTSQVVPSDTMQTRHVKNYHSRSESTVENFLCR
> #SACVFYTTYENHDSDGDNFAYWVINTRQVAQLRRKLEMFTYARFDLELTFVITSTQEQPTVRGQDAPVLT
> #HQIMYVPPGGPVPTKVNSYSWQTSTNPSVFWTEGSAPPRMSVPFIGIGNAYSMFYDGWARFDKQGTYGIS
> #TLNNMGTLYMRHVNDGGPGPIVSTVRIYFKPKHVKTWVPRPPRLCQYQKAGNVNFEPTGVTEGRTDITTM
> #KTT
> 
> However, according to documation Bio::Sequence::Common#to_fasta is a
> deprecated method and it suggests to use Bio::Sequence#output, but when I
> modify code to
> 
> puts seq.output(:fasta)
> 
> it gives error that method is not defined. Also I don't see a way how to
> define the header.
> 
> What should i use in place of the deprecated to_fasta method?
> 
> Thanks,
> 
> Diana
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby




From rozziite at gmail.com  Fri Aug  7 17:31:45 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Fri, 7 Aug 2009 13:31:45 -0400
Subject: [BioRuby] GSOC PhyloXML profiling, bottleneck is Bio::Tree#children
Message-ID: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com>

Hi all,

Here is update on Google Summer of Code Bioruby PhyloXML project. I was
profiling and refactoring Bioruby PhyloXML Parser code and got 67% speed
increase.

With profiling PhyloXML Writer the story is different. It takes 24minutes to
write the 1.5MB mollusca taxonomy tree and forever other larger files.
Again the bottleneck is bfs_shortest_path, which is called from
Tree#children method. It takes forever to just iterate over all the children
nodes.

To solve this I propose to save an array of the children of the node within
my PhyloXML::Node (which corresponds to a clade) class. This would also
ensure that when a phyloxml file is parsed and then written back, clades
would be the same order in the input and output files.


Have a good weekend,

Diana


From czmasek at burnham.org  Fri Aug  7 20:47:31 2009
From: czmasek at burnham.org (Christian Zmasek)
Date: Fri, 7 Aug 2009 13:47:31 -0700
Subject: [BioRuby] GSOC PhyloXML profiling,
	bottleneck is Bio::Tree#children
In-Reply-To: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com>
References: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com>
Message-ID: <E4F65F2E907A6F4B8582E0E44B2505EA326E0005B5@MAIL07.burnham.org>

Hi, Diana:

I think your array based solution is fine.

Although, at one point Bioruby's Tree might need to be enhanced, in order to avoid being slowed down by this bfs_shortest_path method. This issue is likely to prohibit (time-wise) many types of algorithms acting on large tree objects.

Christian


________________________________________
From: Diana Jaunzeikare [rozziite at gmail.com]
Sent: Friday, August 07, 2009 10:31 AM
To: Christian Zmasek; Phyloinformatics Group; Pjotr Prins; bioruby at lists.open-bio.org; Naohisa GOTO
Subject: GSOC PhyloXML profiling, bottleneck is Bio::Tree#children

Hi all,

Here is update on Google Summer of Code Bioruby PhyloXML project. I was profiling and refactoring Bioruby PhyloXML Parser code and got 67% speed increase.

With profiling PhyloXML Writer the story is different. It takes 24minutes to write the 1.5MB mollusca taxonomy tree and forever other larger files.  Again the bottleneck is bfs_shortest_path, which is called from Tree#children method. It takes forever to just iterate over all the children nodes.

To solve this I propose to save an array of the children of the node within my PhyloXML::Node (which corresponds to a clade) class. This would also ensure that when a phyloxml file is parsed and then written back, clades would be the same order in the input and output files.


Have a good weekend,

Diana



From ngoto at gen-info.osaka-u.ac.jp  Mon Aug 10 02:58:12 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 10 Aug 2009 11:58:12 +0900
Subject: [BioRuby] GSOC PhyloXML profiling,
	bottleneck is Bio::Tree#children
In-Reply-To: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com>
References: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com>
Message-ID: <20090810025814.9A8371CBC49D@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Fri, 7 Aug 2009 13:31:45 -0400
Diana Jaunzeikare <rozziite at gmail.com> wrote:

> Hi all,
> 
> Here is update on Google Summer of Code Bioruby PhyloXML project. I was
> profiling and refactoring Bioruby PhyloXML Parser code and got 67% speed
> increase.
> 
> With profiling PhyloXML Writer the story is different. It takes 24minutes to
> write the 1.5MB mollusca taxonomy tree and forever other larger files.
> Again the bottleneck is bfs_shortest_path, which is called from
> Tree#children method. It takes forever to just iterate over all the children
> nodes.

Bio::Tree uses graph algorithm  implemented in the Bio::Pathway class.
As you say, their implementations are naive and should be rewritten
in the future.

> To solve this I propose to save an array of the children of the node within
> my PhyloXML::Node (which corresponds to a clade) class. This would also
> ensure that when a phyloxml file is parsed and then written back, clades
> would be the same order in the input and output files.

How to maintain the array when modifying the tree, e.g. to add,
delete, or replace some nodes and edges?


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


> Have a good weekend,
> 
> Diana
> 


From rozziite at gmail.com  Mon Aug 10 15:00:54 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Mon, 10 Aug 2009 11:00:54 -0400
Subject: [BioRuby] GSOC PhyloXML profiling,
	bottleneck is Bio::Tree#children
In-Reply-To: <20090810025814.9A8371CBC49D@idnmail.gen-info.osaka-u.ac.jp>
References: <4057d3bf0908071031g39e64004t50abceae87e12fed@mail.gmail.com> 
	<20090810025814.9A8371CBC49D@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <4057d3bf0908100800j544d0bcaqa063b0b9f5267a53@mail.gmail.com>

On Sun, Aug 9, 2009 at 10:58 PM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi,
>
> On Fri, 7 Aug 2009 13:31:45 -0400
> Diana Jaunzeikare <rozziite at gmail.com> wrote:
>
> > Hi all,
> >
> > Here is update on Google Summer of Code Bioruby PhyloXML project. I was
> > profiling and refactoring Bioruby PhyloXML Parser code and got 67% speed
> > increase.
> >
> > With profiling PhyloXML Writer the story is different. It takes 24minutes
> to
> > write the 1.5MB mollusca taxonomy tree and forever other larger files.
> > Again the bottleneck is bfs_shortest_path, which is called from
> > Tree#children method. It takes forever to just iterate over all the
> children
> > nodes.
>
> Bio::Tree uses graph algorithm  implemented in the Bio::Pathway class.
> As you say, their implementations are naive and should be rewritten
> in the future.
>
> > To solve this I propose to save an array of the children of the node
> within
> > my PhyloXML::Node (which corresponds to a clade) class. This would also
> > ensure that when a phyloxml file is parsed and then written back, clades
> > would be the same order in the input and output files.
>
> How to maintain the array when modifying the tree, e.g. to add,
> delete, or replace some nodes and edges?
>

I didn't think of this issue. I guess then instead of adding that support in
PhyloXML class I could rewrite Bio::Tree class, thus other projects based on
Bio::Tree class would benefit in the future.

Diana


>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
>
> > Have a good weekend,
> >
> > Diana
> >
>


From rozziite at gmail.com  Mon Aug 10 19:54:55 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Mon, 10 Aug 2009 15:54:55 -0400
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
Message-ID: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>

Hi all,

What was done last week:

* Coding. Added changes so that now it is completely compatible with
phyloxml schema 1.10

* Testing. added more unit tests (now writer has 9 tests, 26 assertions;
parser: 40 tests, 134 assertions)

* Profiling. I discovered that writer is really slow. The reason is the
implementation of the Tree#children method, which does bfs_shortest_path
algorithm. I had idea of tracking node children inside the node class as an
array, but Naohisa Goto pointed out that then I would also have to deal with
new node, edge addition, removal, etc. So better solution seems to, for now
leave it as it is, and first improve Bio::Tree class. I am planning to do
that after GSOC, since there is only one week left.

* Refactored parser class, got around 3-fold speed increase. Now it can
parse Metazoa taxonomy 33MB file in ~14 seconds (Ubuntu 9.04, ruby 1.8.7
[i486-linux], Intel Core 2 Duo P8600 @2.4GHz)

Next week:

* Create howto wiki page with code examples and usage.
* Do more testing (Anybody has some more phyloxml xml files for me to test,
other than those on phyloxml.org?)
* Any other suggestions from you?

Questions/issues:

* Where should the HOWTO and code example documentation go? Seems reasonable
for it to go here
 http://bioruby.open-bio.org/wiki/HOWTO:Trees and/or
http://bioruby.open-bio.org/wiki/Phyloxml_tree_format (which is linked from
previous link).

* How does integration to the master branch goes? Is all i have to do is
pull_request on github?

* I have implemented PhyloXML::Sequence#to_biosequence, however it returns
incomplete data, since info for Bio::Sequence#classification,
Bio::Sequence#species, Bio::Sequence#division would come from
PhyloXML::Taxonomy class, but it is not accessible from Sequence class.
Should there be PhyloXML::Node#to_biosequence method which would gather
information from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
Bio::Sequence should not hold taxonomic information?

You are all welcome to test my code. It is available on
http://github.com/latvianlinuxgirl/bioruby/tree/dev

Thanks,

Diana


From john.woods at marcottelab.org  Fri Aug  7 18:23:22 2009
From: john.woods at marcottelab.org (John O. Woods)
Date: Fri, 7 Aug 2009 13:23:22 -0500
Subject: [BioRuby] Feedback requested on OBO module
Message-ID: <91656c3f0908071123n3f130f29p2a1a33c4db50214d@mail.gmail.com>

Hi all,
I'm pretty new to Ruby (and Rails), first of all. I wrote a simple reader
for OBO files (attached). It does not write (currently), but it can
interface with ActiveRecord and acts-as-dag to create a directed acyclic
graph in a database.

As a newbie, I suspect I'm doing some things wrong, or at least not as
correctly as they could be done. For example, usually rails migrations that
fail undo all of their changes; but I can't figure out how I'd write that. I
attempted to do so, but it apparently does not work (have to set
:save_immediately => true to get it to work).

I'd love some feedback, if anyone would be willing to take a quick look at
my code.

I've also attached a test file from Flybase. An object can be created with:
od = Bio::OboDoc.new("filename.obo")

Thanks!
John

From ngoto at gen-info.osaka-u.ac.jp  Thu Aug 13 08:21:39 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 13 Aug 2009 17:21:39 +0900
Subject: [BioRuby] Feedback requested on OBO module
In-Reply-To: <91656c3f0908071123n3f130f29p2a1a33c4db50214d@mail.gmail.com>
References: <91656c3f0908071123n3f130f29p2a1a33c4db50214d@mail.gmail.com>
Message-ID: <20090813082140.0536D1CBC413@idnmail.gen-info.osaka-u.ac.jp>

Hi,

In this mailing list, attachment files are normally dropped.

To continue discussions, if the code is short, desribe it in the
message body. If it isn't short, put your code on your web site or
on a code repository (for example http://gist.github.com/ ) and
post only the URL.

Thanks.

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

On Fri, 7 Aug 2009 13:23:22 -0500
"John O. Woods" <john.woods at marcottelab.org> wrote:

> Hi all,
> I'm pretty new to Ruby (and Rails), first of all. I wrote a simple reader
> for OBO files (attached). It does not write (currently), but it can
> interface with ActiveRecord and acts-as-dag to create a directed acyclic
> graph in a database.
> 
> As a newbie, I suspect I'm doing some things wrong, or at least not as
> correctly as they could be done. For example, usually rails migrations that
> fail undo all of their changes; but I can't figure out how I'd write that. I
> attempted to do so, but it apparently does not work (have to set
> :save_immediately => true to get it to work).
> 
> I'd love some feedback, if anyone would be willing to take a quick look at
> my code.
> 
> I've also attached a test file from Flybase. An object can be created with:
> od = Bio::OboDoc.new("filename.obo")
> 
> Thanks!
> John
> 



From rozziite at gmail.com  Thu Aug 13 21:50:01 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Thu, 13 Aug 2009 17:50:01 -0400
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
Message-ID: <4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>

Hi all,

I added here a HOWTO for BioRuby PhyloXML implementation

https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation

Let me know, what you think

Diana

On Mon, Aug 10, 2009 at 3:54 PM, Diana Jaunzeikare <rozziite at gmail.com>wrote:

> Hi all,
>
> What was done last week:
>
> * Coding. Added changes so that now it is completely compatible with
> phyloxml schema 1.10
>
> * Testing. added more unit tests (now writer has 9 tests, 26 assertions;
> parser: 40 tests, 134 assertions)
>
> * Profiling. I discovered that writer is really slow. The reason is the
> implementation of the Tree#children method, which does bfs_shortest_path
> algorithm. I had idea of tracking node children inside the node class as an
> array, but Naohisa Goto pointed out that then I would also have to deal with
> new node, edge addition, removal, etc. So better solution seems to, for now
> leave it as it is, and first improve Bio::Tree class. I am planning to do
> that after GSOC, since there is only one week left.
>
> * Refactored parser class, got around 3-fold speed increase. Now it can
> parse Metazoa taxonomy 33MB file in ~14 seconds (Ubuntu 9.04, ruby 1.8.7
> [i486-linux], Intel Core 2 Duo P8600 @2.4GHz)
>
> Next week:
>
> * Create howto wiki page with code examples and usage.
> * Do more testing (Anybody has some more phyloxml xml files for me to test,
> other than those on phyloxml.org?)
> * Any other suggestions from you?
>
> Questions/issues:
>
> * Where should the HOWTO and code example documentation go? Seems
> reasonable for it to go here
>  http://bioruby.open-bio.org/wiki/HOWTO:Trees and/or
> http://bioruby.open-bio.org/wiki/Phyloxml_tree_format (which is linked
> from previous link).
>
> * How does integration to the master branch goes? Is all i have to do is
> pull_request on github?
>
> * I have implemented PhyloXML::Sequence#to_biosequence, however it returns
> incomplete data, since info for Bio::Sequence#classification,
> Bio::Sequence#species, Bio::Sequence#division would come from
> PhyloXML::Taxonomy class, but it is not accessible from Sequence class.
> Should there be PhyloXML::Node#to_biosequence method which would gather
> information from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
> Bio::Sequence should not hold taxonomic information?
>
> You are all welcome to test my code. It is available on
> http://github.com/latvianlinuxgirl/bioruby/tree/dev
>
> Thanks,
>
> Diana
>


From czmasek at burnham.org  Fri Aug 14 18:41:13 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Fri, 14 Aug 2009 11:41:13 -0700
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
	<4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
Message-ID: <4A85AFC9.4020106@burnham.org>

Very nice!!

I guess this will be placed/copied to the BioRuby tutorial (at 
http://bioruby.open-bio.org/wiki/Tutorial) at one point, correct?



A very tiny, minuscule even, issue I noticed (and maybe even a problem 
of my web browser):

A the very end, the blue box seems broken at the "wrong place" -- so to 
speak, i.e.

"#Once we know whats there, lets output just sequences
phyloxml.other[0].children.each do |node|
   puts node.value
end"

and

"#=>
#
#acgtcgcggcccgtggaagtcctctcct
#aggtcgcggcctgtggaagtcctctcct
#taaatcgc--cccgtgg-agtccc-cct"

should be in the same box, but they appear to be in different ones.

Christian





Diana Jaunzeikare wrote:
> Hi all,
> 
> I added here a HOWTO for BioRuby PhyloXML implementation
> 
> https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
> 
> Let me know, what you think
> 
> Diana
> 
> On Mon, Aug 10, 2009 at 3:54 PM, Diana Jaunzeikare <rozziite at gmail.com 
> <mailto:rozziite at gmail.com>> wrote:
> 
>     Hi all,
> 
>     What was done last week:
> 
>     * Coding. Added changes so that now it is completely compatible with
>     phyloxml schema 1.10
> 
>     * Testing. added more unit tests (now writer has 9 tests, 26
>     assertions; parser: 40 tests, 134 assertions)
> 
>     * Profiling. I discovered that writer is really slow. The reason is
>     the implementation of the Tree#children method, which does
>     bfs_shortest_path algorithm. I had idea of tracking node children
>     inside the node class as an array, but Naohisa Goto pointed out that
>     then I would also have to deal with new node, edge addition,
>     removal, etc. So better solution seems to, for now leave it as it
>     is, and first improve Bio::Tree class. I am planning to do that
>     after GSOC, since there is only one week left.
> 
>     * Refactored parser class, got around 3-fold speed increase. Now it
>     can parse Metazoa taxonomy 33MB file in ~14 seconds (Ubuntu 9.04,
>     ruby 1.8.7 [i486-linux], Intel Core 2 Duo P8600 @2.4GHz)
> 
>     Next week:
> 
>     * Create howto wiki page with code examples and usage.
>     * Do more testing (Anybody has some more phyloxml xml files for me
>     to test, other than those on phyloxml.org <http://phyloxml.org>?)
>     * Any other suggestions from you?
> 
>     Questions/issues:
> 
>     * Where should the HOWTO and code example documentation go? Seems
>     reasonable for it to go here
>      http://bioruby.open-bio.org/wiki/HOWTO:Trees and/or
>     http://bioruby.open-bio.org/wiki/Phyloxml_tree_format (which is
>     linked from previous link).
> 
>     * How does integration to the master branch goes? Is all i have to
>     do is pull_request on github?
> 
>     * I have implemented PhyloXML::Sequence#to_biosequence, however it
>     returns incomplete data, since info for
>     Bio::Sequence#classification, Bio::Sequence#species,
>     Bio::Sequence#division would come from PhyloXML::Taxonomy class, but
>     it is not accessible from Sequence class. Should there be
>     PhyloXML::Node#to_biosequence method which would gather information
>     from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
>     Bio::Sequence should not hold taxonomic information?
> 
>     You are all welcome to test my code. It is available on
>     http://github.com/latvianlinuxgirl/bioruby/tree/dev
> 
>     Thanks,
> 
>     Diana
> 
> 



From czmasek at burnham.org  Fri Aug 14 18:52:04 2009
From: czmasek at burnham.org (Christian M Zmasek)
Date: Fri, 14 Aug 2009 11:52:04 -0700
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
	<4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
Message-ID: <4A85B254.8020601@burnham.org>

Hi, Diana:

> 
>     * How does integration to the master branch goes? Is all i have to
>     do is pull_request on github?

I think so (never done this myself, though). Maybe the git experts can 
answer this?


>     * I have implemented PhyloXML::Sequence#to_biosequence, however it
>     returns incomplete data, since info for
>     Bio::Sequence#classification, Bio::Sequence#species,
>     Bio::Sequence#division would come from PhyloXML::Taxonomy class, but
>     it is not accessible from Sequence class. Should there be
>     PhyloXML::Node#to_biosequence method which would gather information
>     from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
>     Bio::Sequence should not hold taxonomic information?

Good point. Personally, I would leave your 
PhyloXML::Sequence#to_biosequence as it is (and add a warning about this 
  to the documentation) and, in addition, create 
PhyloXML::Node#to_biosequence -- although, I would not call it 
to_biosequence but maybe something like extract_biosequence.
Needless to say, that an almost infinite number of "solutions" to this 
exists, without a clear "winner" (in my opinion).

Christian



From ngoto at gen-info.osaka-u.ac.jp  Sat Aug 15 10:38:24 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Sat, 15 Aug 2009 19:38:24 +0900
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4A85B254.8020601@burnham.org>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
	<4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
	<4A85B254.8020601@burnham.org>
Message-ID: <20090815103824.DEC901CBC494@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Fri, 14 Aug 2009 11:52:04 -0700
Christian M Zmasek <czmasek at burnham.org> wrote:

> Hi, Diana:
> 
> > 
> >     * How does integration to the master branch goes? Is all i have to
> >     do is pull_request on github?
> 
> I think so (never done this myself, though). Maybe the git experts can 
> answer this?

I'll soon release 1.3.1, bug-fix release of 1.3.0.
After that, the PhyloXML support and some other new functions
such as Chromatogram class http://github.com/aunderwo/bioruby/tree
will be merged, and will be released as 1.4.0.

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


From andrew.j.grimm at gmail.com  Sun Aug 16 10:42:23 2009
From: andrew.j.grimm at gmail.com (Andrew Grimm)
Date: Sun, 16 Aug 2009 20:42:23 +1000
Subject: [BioRuby] Code style question
Message-ID: <b9140daa0908160342s7d12abebk94c4ab1303f212ee@mail.gmail.com>

The Readme for developers mentions that

  if __FILE__ == $0

is deprecated for testing.

In lib/bio/db/fasta.rb , there's a __FILE__ == $0 that isn't used for
testing, but for demonstrating what the module's supposed to do. Is
this kind of coding non-deprecated?

Andrew


From ngoto at gen-info.osaka-u.ac.jp  Sun Aug 16 12:57:10 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto)
Date: Sun, 16 Aug 2009 21:57:10 +0900
Subject: [BioRuby] Code style question
In-Reply-To: <b9140daa0908160342s7d12abebk94c4ab1303f212ee@mail.gmail.com>
References: <b9140daa0908160342s7d12abebk94c4ab1303f212ee@mail.gmail.com>
Message-ID: <20090816215623.4B48.EEF6E030@gen-info.osaka-u.ac.jp>

Hi,

> The Readme for developers mentions that
> 
>   if __FILE__ == $0
> 
> is deprecated for testing.
> 
> In lib/bio/db/fasta.rb , there's a __FILE__ == $0 that isn't used for
> testing, but for demonstrating what the module's supposed to do. Is
> this kind of coding non-deprecated?
> 
> Andrew

Yes, deprecated for new codes. 

Old codes before the style have been deprecated may be existed.
We gradually move and rewrite them to unit tests and/or sample codes.

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




From rozziite at gmail.com  Sun Aug 16 20:09:49 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Sun, 16 Aug 2009 16:09:49 -0400
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4A85B254.8020601@burnham.org>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com> 
	<4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com> 
	<4A85B254.8020601@burnham.org>
Message-ID: <4057d3bf0908161309p634fd95bt24b81debe9b2a669@mail.gmail.com>

On Fri, Aug 14, 2009 at 2:52 PM, Christian M Zmasek <czmasek at burnham.org>wrote:

> Hi, Diana:
>
>
>>    * How does integration to the master branch goes? Is all i have to
>>    do is pull_request on github?
>>
>
> I think so (never done this myself, though). Maybe the git experts can
> answer this?
>
>
>     * I have implemented PhyloXML::Sequence#to_biosequence, however it
>>    returns incomplete data, since info for
>>    Bio::Sequence#classification, Bio::Sequence#species,
>>    Bio::Sequence#division would come from PhyloXML::Taxonomy class, but
>>    it is not accessible from Sequence class. Should there be
>>    PhyloXML::Node#to_biosequence method which would gather information
>>    from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
>>    Bio::Sequence should not hold taxonomic information?
>>
>
> Good point. Personally, I would leave your
> PhyloXML::Sequence#to_biosequence as it is (and add a warning about this  to
> the documentation) and, in addition, create PhyloXML::Node#to_biosequence --
> although, I would not call it to_biosequence but maybe something like
> extract_biosequence.
> Needless to say, that an almost infinite number of "solutions" to this
> exists, without a clear "winner" (in my opinion).
>
> Christian
>
>
I added PhyloXML::Node#extract_biosequence method. It first calls
sequence#to_biosequence and then adds additional information from taxonomy
elements.

Diana


From czmasek at burnham.org  Mon Aug 17 01:57:06 2009
From: czmasek at burnham.org (Christian Zmasek)
Date: Sun, 16 Aug 2009 18:57:06 -0700
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4057d3bf0908161309p634fd95bt24b81debe9b2a669@mail.gmail.com>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
	<4057d3bf0908131450v54583bc2ve9bd3f0057d634e0@mail.gmail.com>
	<4A85B254.8020601@burnham.org>,
	<4057d3bf0908161309p634fd95bt24b81debe9b2a669@mail.gmail.com>
Message-ID: <E4F65F2E907A6F4B8582E0E44B2505EA32FBA3456A@MAIL07.burnham.org>

Sounds very good!

________________________________________
From: Diana Jaunzeikare [rozziite at gmail.com]
Sent: Sunday, August 16, 2009 1:09 PM
To: Christian Zmasek
Cc: bioruby at lists.open-bio.org; Pjotr Prins; Naohisa GOTO; Phyloinformatics Group
Subject: Re: GSOC: Bioruby PhyloXML update 12

On Fri, Aug 14, 2009 at 2:52 PM, Christian M Zmasek <czmasek at burnham.org<mailto:czmasek at burnham.org>> wrote:
Hi, Diana:



   * How does integration to the master branch goes? Is all i have to
   do is pull_request on github?

I think so (never done this myself, though). Maybe the git experts can answer this?



   * I have implemented PhyloXML::Sequence#to_biosequence, however it
   returns incomplete data, since info for
   Bio::Sequence#classification, Bio::Sequence#species,
   Bio::Sequence#division would come from PhyloXML::Taxonomy class, but
   it is not accessible from Sequence class. Should there be
   PhyloXML::Node#to_biosequence method which would gather information
   from both PhyloXML::Sequence and PhyloXML::Taxonomy? or maybe
   Bio::Sequence should not hold taxonomic information?

Good point. Personally, I would leave your PhyloXML::Sequence#to_biosequence as it is (and add a warning about this  to the documentation) and, in addition, create PhyloXML::Node#to_biosequence -- although, I would not call it to_biosequence but maybe something like extract_biosequence.
Needless to say, that an almost infinite number of "solutions" to this exists, without a clear "winner" (in my opinion).

Christian


I added PhyloXML::Node#extract_biosequence method. It first calls sequence#to_biosequence and then adds additional information from taxonomy elements.

Diana




From rozziite at gmail.com  Mon Aug 17 15:20:45 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Mon, 17 Aug 2009 11:20:45 -0400
Subject: [BioRuby] Bioruby PhyloXML pencils down
Message-ID: <4057d3bf0908170820g552389d7r958a52af3f62b7d5@mail.gmail.com>

Hi all,

So the Google Summer of Code is over. I had a great time learning and
improving my programming skills in real world environment. Especially I am
glad that I learned more of "doing things in the ruby way".  I think that
writing open source will definitely help me to land with a better job after
graduation since the result is something i can actually show to the
potential employers as example of my work.

Here is the summary:

* Wrote Bio::PhyloXML::Parser class which is responsible for parsing xml
files in phyloxml format. It inherits from Bio::Tree and thus have all the
functionality Bio::Tree class have.

* Wrote Bio::PhyloXML::Writer class which is responsible for writing
(hopefully) valid xml files against phyloxml schema. For most part it
produces xml files that validate against phyloxml schema, but probably it is
possible to produce artificial example when it is not, since not everywhere
i have checks for valid input or data type. This is where i can improve in
future.

* Since these classes are meant to deal with big data files, I changed code
several times to make it faster. I managed to improve the speed of the
Parser by a lot, but not for the Writer. In order to improve speed of the
Writer, i will first improve the underlying Bio::Tree class (thus others
also might benefit from faster Bio::Tree class).

* Bio::PhyloXML module holds classes corresponding to complex phyloxml
elements. Here http://wiki.github.com/latvianlinuxgirl/bioruby is the design
of classes.

* The code is here http://github.com/latvianlinuxgirl/bioruby/tree/dev

* The project page is here:
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby,
where probably I will continue to post future plan.

* Code examples are
https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation.
The same information is also incorporated in bioruby tutorial.


I will definitely stay involved in BioRuby and open source community. The
next step will be to improve Bio::Tree class, especially Bio::Tree#parent
and Bio::Tree#children methods. Next semester I will be taking Algorithms
class, so maybe I will be able to apply that knowledge to this task.  And of
course I plan to maintain my code, since when people will start using the
code, bugs will start to creep up.

I would like to thank my mentors Christian and Pjotr for support and timely
answers to my questions. Also thanks to Naohisa and others who answered my
questions and helped me.

Diana


From john.woods at marcottelab.org  Sat Aug 22 00:04:03 2009
From: john.woods at marcottelab.org (John O. Woods)
Date: Fri, 21 Aug 2009 19:04:03 -0500
Subject: [BioRuby] Batch Entrez search
Message-ID: <91656c3f0908211704p5b97f909ve168f4fcb7873fee@mail.gmail.com>

Right now I'm doing, one at a time: n.search("gene", "FBgn0041721")I'm
trying to get the gene ID corresponding to a Flybase gene ID.

This takes forever, since you can only do one every three seconds.

Also, sometimes it returns two items, and one might be deprecated--but
there's no way to tell.

Is there a way to batch search with BioRuby for a whole bunch of Flybase
IDs?

Many thanks,
John

Marcotte Lab | The University of Texas at Austin


From tomoakin at kenroku.kanazawa-u.ac.jp  Mon Aug 24 02:21:18 2009
From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA)
Date: Mon, 24 Aug 2009 11:21:18 +0900
Subject: [BioRuby] Batch Entrez search
In-Reply-To: <91656c3f0908211704p5b97f909ve168f4fcb7873fee@mail.gmail.com>
References: <91656c3f0908211704p5b97f909ve168f4fcb7873fee@mail.gmail.com>
Message-ID: <AB3385C8-0DE1-4F42-8532-CA128EA2B140@kenroku.kanazawa-u.ac.jp>

Hi,

> Is there a way to batch search with BioRuby for a whole bunch of  
> Flybase
> IDs?


According to
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpgene&part=genefaq
the data for entrez gene are available in
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

If you need really a lot, perhaps its better to download that file  
(about 93 Mbytes).
(It contains data for other organisms, which is not necessary, but  
does not take forever)
The format seems simple enough that you can easily get the gene ID  
for a flybase ID.

#Format: tax_id GeneID Symbol LocusTag Synonyms dbXrefs chromosome  
map_location description type_of_gene  
Symbol_from_nomenclature_authority Full_name_from_nomenclatur
e_authority Nomenclature_status Other_designations Modification_date  
(tab is used as a separator, pound sign - start of a comment)

-- 
Tomoaki NISHIYAMA

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



From marc.hoeppner at molbio.su.se  Mon Aug 24 05:36:48 2009
From: marc.hoeppner at molbio.su.se (Marc Hoeppner)
Date: Mon, 24 Aug 2009 07:36:48 +0200
Subject: [BioRuby] Batch Entrez search
In-Reply-To: <AB3385C8-0DE1-4F42-8532-CA128EA2B140@kenroku.kanazawa-u.ac.jp>
References: <91656c3f0908211704p5b97f909ve168f4fcb7873fee@mail.gmail.com>
	<AB3385C8-0DE1-4F42-8532-CA128EA2B140@kenroku.kanazawa-u.ac.jp>
Message-ID: <4A9226F0.4050206@molbio.su.se>

Hi,

I suppose for FlyBase genes you could also use the ruby Ensembl API.

Something like:

require 'ensembl'


Ensembl::Core::DBConnection('drosophila_melanogaster','55)

IO.foreach('my_infile') do |flybase_id|

    gene = Ensembl::Core::Gene.find_by_stable_id(flybase_id)
   
    gene.all_xrefs.each do |xref|
      
        puts xref
   
    end

end

Well, you get the idea. The methods are well documented in the 
corresponding API, but when in doubt I can offer some help, too.

P.S.: To make it real easy you could also use the BioMart on 
www.ensembl.org - unless you need this to be a script.

Cheers,

Marc
> Hi,
>
>> Is there a way to batch search with BioRuby for a whole bunch of Flybase
>> IDs?
>
>
> According to
> http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpgene&part=genefaq
> the data for entrez gene are available in
> ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
>
> If you need really a lot, perhaps its better to download that file 
> (about 93 Mbytes).
> (It contains data for other organisms, which is not necessary, but 
> does not take forever)
> The format seems simple enough that you can easily get the gene ID for 
> a flybase ID.
>
> #Format: tax_id GeneID Symbol LocusTag Synonyms dbXrefs chromosome 
> map_location description type_of_gene 
> Symbol_from_nomenclature_authority Full_name_from_nomenclatur
> e_authority Nomenclature_status Other_designations Modification_date 
> (tab is used as a separator, pound sign - start of a comment)
>


-- 

Marc P. Hoeppner
PhD student
Department of Molecular Biology and Functional Genomics
Stockholm University, 10691 Stockholm, Sweden

marc.hoeppner at molbio.su.se
Tel: +46 (0)8 - 164195



From john.woods at marcottelab.org  Mon Aug 24 12:44:31 2009
From: john.woods at marcottelab.org (John O. Woods)
Date: Mon, 24 Aug 2009 07:44:31 -0500
Subject: [BioRuby] Batch Entrez search
In-Reply-To: <4A9226F0.4050206@molbio.su.se>
References: <91656c3f0908211704p5b97f909ve168f4fcb7873fee@mail.gmail.com>
	<AB3385C8-0DE1-4F42-8532-CA128EA2B140@kenroku.kanazawa-u.ac.jp>
	<4A9226F0.4050206@molbio.su.se>
Message-ID: <91656c3f0908240544h20577825n38817c7667081b90@mail.gmail.com>

Unfortunately, many Flybase IDs seem to be missing from BioMart, which leads
me to think they'd also be absent from Ensembl.

On Mon, Aug 24, 2009 at 12:36 AM, Marc Hoeppner
<marc.hoeppner at molbio.su.se>wrote:

> Hi,
>
> I suppose for FlyBase genes you could also use the ruby Ensembl API.
>
> Something like:
>
> require 'ensembl'
>
>
> Ensembl::Core::DBConnection('drosophila_melanogaster','55)
>
> IO.foreach('my_infile') do |flybase_id|
>
>   gene = Ensembl::Core::Gene.find_by_stable_id(flybase_id)
>     gene.all_xrefs.each do |xref|
>           puts xref
>     end
>
> end
>
> Well, you get the idea. The methods are well documented in the
> corresponding API, but when in doubt I can offer some help, too.
>
> P.S.: To make it real easy you could also use the BioMart on
> www.ensembl.org - unless you need this to be a script.
>
> Cheers,
>
> Marc
>
>> Hi,
>>
>>  Is there a way to batch search with BioRuby for a whole bunch of Flybase
>>> IDs?
>>>
>>
>>
>> According to
>> http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpgene&part=genefaq
>> the data for entrez gene are available in
>> ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz
>>
>> If you need really a lot, perhaps its better to download that file (about
>> 93 Mbytes).
>> (It contains data for other organisms, which is not necessary, but does
>> not take forever)
>> The format seems simple enough that you can easily get the gene ID for a
>> flybase ID.
>>
>> #Format: tax_id GeneID Symbol LocusTag Synonyms dbXrefs chromosome
>> map_location description type_of_gene Symbol_from_nomenclature_authority
>> Full_name_from_nomenclatur
>> e_authority Nomenclature_status Other_designations Modification_date (tab
>> is used as a separator, pound sign - start of a comment)
>>
>>
>
> --
>
> Marc P. Hoeppner
> PhD student
> Department of Molecular Biology and Functional Genomics
> Stockholm University, 10691 Stockholm, Sweden
>
> marc.hoeppner at molbio.su.se
> Tel: +46 (0)8 - 164195
>
>


From biopython at maubp.freeserve.co.uk  Thu Aug 27 10:46:17 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 27 Aug 2009 11:46:17 +0100
Subject: [BioRuby] FASTQ in BioRuby?
Message-ID: <320fb6e00908270346y5d653d29mdd2dc7ebc76af3c1@mail.gmail.com>

Hello BioRuby team,

I am one of the Biopython developers, and together with Peter Rice
(EMBOSS) and Chris Fields (BioPerl) we have been coordinating
how these Open Bioinformatics Foundation (OBF) projects will
interpret the FASTQ file format used in next generation sequencing.

This includes standardising our naming conventions for the original
Sanger FASTQ variant, and the later Solexa/early Illumina, and
recent Illumina 1.3+ variants. We have also put together a set of
test files, including reference conversions between the different
FASTQ variants.

We would be delighted to get BioRuby involved. I tried to contact
Naohisa Goto about this directly last month, but perhaps my email
did not arrive. If BioRuby is working on (or planning to work on)
FASTQ support, please could the developers concerned sign up
to the OBF joint mailing list where we have been discussing this:
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thank you,

Peter


From ngoto at gen-info.osaka-u.ac.jp  Thu Aug 27 11:20:46 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 27 Aug 2009 20:20:46 +0900
Subject: [BioRuby] [Open-bio-l] FASTQ in BioRuby?
In-Reply-To: <320fb6e00908270346y5d653d29mdd2dc7ebc76af3c1@mail.gmail.com>
References: <320fb6e00908270346y5d653d29mdd2dc7ebc76af3c1@mail.gmail.com>
Message-ID: <20090827112046.E2C741CBC4BA@idnmail.gen-info.osaka-u.ac.jp>

Hello Peter,

sorry for responding too late. I've subscribed to open-bio-l,
but I could not actively join to the discussions, because of
lack of my knowledge about FASTQ.

There is a small primitive code attempt to support FASTQ format
in BioRuby, which is not yet merged in the main repository.
http://github.com/ngoto/bioruby/tree/master

Recently, Anthony Underwood contributed chromatgram classes
to support SCF/ABI formats, which will be merged soon,
after bug-fix maintenance release of 1.3.1.
http://github.com/aunderwo/bioruby/tree/master

I'm now planning to rewrite my FASTQ code to be consistent
with the chromatgram classes, and with the open-bio standards.

Thank you,

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

On Thu, 27 Aug 2009 11:46:17 +0100
Peter <biopython at maubp.freeserve.co.uk> wrote:

> Hello BioRuby team,
> 
> I am one of the Biopython developers, and together with Peter Rice
> (EMBOSS) and Chris Fields (BioPerl) we have been coordinating
> how these Open Bioinformatics Foundation (OBF) projects will
> interpret the FASTQ file format used in next generation sequencing.
> 
> This includes standardising our naming conventions for the original
> Sanger FASTQ variant, and the later Solexa/early Illumina, and
> recent Illumina 1.3+ variants. We have also put together a set of
> test files, including reference conversions between the different
> FASTQ variants.
> 
> We would be delighted to get BioRuby involved. I tried to contact
> Naohisa Goto about this directly last month, but perhaps my email
> did not arrive. If BioRuby is working on (or planning to work on)
> FASTQ support, please could the developers concerned sign up
> to the OBF joint mailing list where we have been discussing this:
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
> 
> Thank you,
> 
> Peter
> _______________________________________________
> Open-Bio-l mailing list
> Open-Bio-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/open-bio-l



From biopython at maubp.freeserve.co.uk  Thu Aug 27 12:08:28 2009
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 27 Aug 2009 13:08:28 +0100
Subject: [BioRuby] [Open-bio-l] FASTQ in BioRuby?
In-Reply-To: <20090827112046.E2C741CBC4BA@idnmail.gen-info.osaka-u.ac.jp>
References: <320fb6e00908270346y5d653d29mdd2dc7ebc76af3c1@mail.gmail.com>
	<20090827112046.E2C741CBC4BA@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <320fb6e00908270508o485ba990k96b8bd3b722c09b6@mail.gmail.com>

On Thu, Aug 27, 2009 at 12:20 PM, Naohisa
GOTO<ngoto at gen-info.osaka-u.ac.jp> wrote:
>
> Hello Peter,
>
> sorry for responding too late. I've subscribed to open-bio-l,
> but I could not actively join to the discussions, because of
> lack of my knowledge about FASTQ.
>
> There is a small primitive code attempt to support FASTQ format
> in BioRuby, which is not yet merged in the main repository.
> http://github.com/ngoto/bioruby/tree/master
>
> Recently, Anthony Underwood contributed chromatgram classes
> to support SCF/ABI formats, which will be merged soon,
> after bug-fix maintenance release of 1.3.1.
> http://github.com/aunderwo/bioruby/tree/master
>
> I'm now planning to rewrite my FASTQ code to be consistent
> with the chromatgram classes, and with the open-bio standards.
>
> Thank you,
>
> Naohisa Goto

That is excellent news :)

I'm not sure how format names work in BioRuby, but if you
do have a set of format names as strings as we do in
Biopython, BioPerl and EMBOSS it would be nice to be
consistent here:

http://biopython.org/wiki/SeqIO
http://bioperl.org/wiki/HOWTO:SeqIO
http://emboss.sourceforge.net/docs/themes/SequenceFormats.html

There is some basic information on wikipedia, but this
does not go into detail:
http://www.bioperl.org/wiki/FASTQ_sequence_format

Please feel free to ask any questions about how we are
interpreting things.

Thank you,

Peter


From ngoto at gen-info.osaka-u.ac.jp  Mon Aug 31 14:22:11 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 31 Aug 2009 23:22:11 +0900
Subject: [BioRuby] SIM4 parser
In-Reply-To: <0C3F8576-899A-426E-869A-C9DCF8F47868@kenroku.kanazawa-u.ac.jp>
References: <5510B566-E723-4AEE-8DEC-63BE1ABD9F19@kenroku.kanazawa-u.ac.jp>
	<0C3F8576-899A-426E-869A-C9DCF8F47868@kenroku.kanazawa-u.ac.jp>
Message-ID: <20090831142212.3468E1CBC58D@idnmail.gen-info.osaka-u.ac.jp>

Hi,

On Sun, 5 Jul 2009 20:28:33 +0900
Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp> wrote:

> Hi,
> 
> > A way to resolve may to check if the start address match the  
> > address that
> > was specified in the previous section stating the ranges of the  
> > matches.
> > I'm considering implementing this way.
> 
> 
> A working code is obtained and a diff relative to 1.3.0 is attached.
> The code was changed to parse alignment only after the SegemntPairs
> are prepared

The bug is fixed.
http://github.com/bioruby/bioruby/commit/02d531e36ecf789f232cf3e05f85391b60279f00

Thank you for sending a patch. I didn't fully use your patch,
but it was very helpful.

> During this work, I also noticed that the semantics of the structure
> might be misunderstood:
> 1. The mark after the match, either "->", "<-", "--", or "=="
> does not represent the direction of the exon, but indicates
>   the presumed direction of the intron following the exon.
> "--" corresponds in case part of the intervening sequence
> and midline is shown and
> "==" is for cases without information for intervening sequence.
> I do not understand how these patterns are determined by SIM4,
> but "->" and "<-" can be estimated based on GU-AG rule.
> Since these directions are essentially assigned to the
> introns rather than exons, it might be inappropriate to assign
> these strings to the exon.  There is actually rare cases that
> introns in different direction is deduced: in such case
> assuming the direction of the exon is same as the 3' intron
> rather than 5' intron of the exon is not desired.  So, it seems
> arguable to make directions for exon deprecated.
>
>  From current state of the parser, I bet there are few people using
> bioruby to parse sim4 alignment output, and changing the interface
> is acceptable this time.

You are right. However, currently, to keep compatibility,
the method Bio::Sim4::Report::SegmentPair#direction is still
being used.  In next major release (1.4.0?), the method will
be deprecated, and other method would be added.

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