From daniel.lundin at molbio.su.se  Mon Jan  8 03:31:08 2007
From: daniel.lundin at molbio.su.se (Daniel Lundin)
Date: Mon, 8 Jan 2007 09:31:08 +0100
Subject: [BioRuby] Is anyone parsing Nexus files?
Message-ID: <20070108083108.GA3246@molbio237.molbio.su.se>

Hi,

I'm new to the list and haven't seen any traffic yet so this is an
activity test as well as a query.

Is anyone on the list parsing Nexus files with Ruby? I couldn't find
anything on the web, so I've been coding a parser myself for the last
couple of days, so if there's anyone interested in sharing the
effort...

My first design goal is to be able to parse a file and write it out
completely in Nexus again, in (more or less) the original format,
without more than basic validation of format (BEGIN - END, semicolons
after statements etc.).  Secondly I have a ``framework'' for adding
classes that more fully parses certain blocks and statements I
personally have an interest in.

I'm afraid I'm rather new to Ruby, so the code is probably not
idiomatically typical.

/Daniel

-- 
Daniel Lundin

Department of Molecular Biology & Functional Genomics
Arrhenius Laboratories for Natural Sciences
Stockholm University, SE-106 91 Stockholm, Sweden

tel. +46 (0)8 16 41 95, mobile: +46 (0)708 123 922, fax. +46 (0)8 16 64 88

Email: daniel.lundin at molbio.su.se

From ngoto at gen-info.osaka-u.ac.jp  Mon Jan  8 10:57:38 2007
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto)
Date: Tue, 09 Jan 2007 00:57:38 +0900
Subject: [BioRuby] Is anyone parsing Nexus files?
In-Reply-To: <20070108083108.GA3246@molbio237.molbio.su.se>
References: <20070108083108.GA3246@molbio237.molbio.su.se>
Message-ID: <20070109004022.3E6B.NGOTO@gen-info.osaka-u.ac.jp>

Hi,

> Hi,
> 
> I'm new to the list and haven't seen any traffic yet so this is an
> activity test as well as a query.
> 
> Is anyone on the list parsing Nexus files with Ruby? I couldn't find
> anything on the web, so I've been coding a parser myself for the last
> couple of days, so if there's anyone interested in sharing the
> effort...

In December, Nexus parser was added to the CVS repository.
It will be available in the next release.

Nexus parser:
http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/lib/bio/db/nexus.rb?rev=HEAD&cvsroot=bioruby&content-type=text/plain

Unit test for the Nexus parser:
http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/test/unit/bio/db/test_nexus.rb?rev=HEAD&cvsroot=bioruby&content-type=text/plain

Your contribution is welcomed.

Sincerely, 

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp


From chen_li3 at yahoo.com  Sat Jan 27 09:23:39 2007
From: chen_li3 at yahoo.com (chen li)
Date: Sat, 27 Jan 2007 06:23:39 -0800 (PST)
Subject: [BioRuby] Download BioRuby API document
Message-ID: <839897.12672.qm@web36804.mail.mud.yahoo.com>

Hi all,

I am new to this forum. I wonder if I can download the
BioRuby's API document and install it to my computer 

Thanks,


Li


 
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