From jan.aerts at bbsrc.ac.uk  Mon Jun  5 06:14:22 2006
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Mon, 5 Jun 2006 11:14:22 +0100
Subject: [BioRuby] classes for chromosomes, genes, exons, polymorphisms, ...
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DADA5@rie2ksrv1.ri.bbsrc.ac.uk>

All,

As far as I know, there are no classes that describe biological concepts
such as 'a chromosome', or 'a gene', or 'an exon'. I'm working out if I
need these things for my own purposes, but wonder if it would be
worthwhile to include them into bioruby? I was thinking of something
like:
  Bio::Entity::Chromosome
  Bio::Entity::Gene
  Bio::Entity::Exon
  Bio::Entity::Repeat
  Bio::Entity::Polymorphism
    Bio::Entity::SNP
    Bio::Entity::Microsatellite

I don't know if Bio::Entity::Chromosome would be necessary, because its
principal use would be to holds annotations (i.e. act as a map), so I
suppose that Bio::Map::SimpleMap could be instead...

Bio::Entity::Gene would include Bio::Map::ActsAsMarker and
Bio::Map::ActsLikeMap, so that a gene can be mapped to something like a
chromosome, but it can also have exons or polymorphisms mapped to it.

Worth to pursue this? And if so: any ideas/comments welcome...

Jan Aerts, PhD
Bioinformatics Group
Roslin Institute
Roslin, Scotland, UK
+44 131 527 4200

---------The obligatory disclaimer--------
The information contained in this e-mail (including any attachments) is
confidential and is intended for the use of the addressee only.   The
opinions expressed within this e-mail (including any attachments) are
the opinions of the sender and do not necessarily constitute those of
Roslin Institute (Edinburgh) ("the Institute") unless specifically
stated by a sender who is duly authorised to do so on behalf of the
Institute. 


From ahr6y at virginia.edu  Mon Jun  5 14:00:56 2006
From: ahr6y at virginia.edu (Anoop Ranganath)
Date: Mon, 5 Jun 2006 14:00:56 -0400
Subject: [BioRuby] adding a flatfile format
Message-ID: <CF8F3F39-4182-4BF0-BE5E-C162BAFF2E48@virginia.edu>

I'd like to add a simple flatfile format to use with bioruby.  In  
particular, I'm looking at BED files, which have a very simple tab  
delimited format.  I'm poking around in the code, and haven't been  
able to find a good example of how to incorporate a new parser.  I'm  
not so much interested in adding support for autodetection, so I  
can't imagine that it would be too difficult.

Does anyone have a starting point I can use?

Thanks,
Anoop 

From ngoto at gen-info.osaka-u.ac.jp  Mon Jun 12 05:56:58 2006
From: ngoto at gen-info.osaka-u.ac.jp (GOTO Naohisa)
Date: Mon, 12 Jun 2006 18:56:58 +0900
Subject: [BioRuby] adding a flatfile format
In-Reply-To: <CF8F3F39-4182-4BF0-BE5E-C162BAFF2E48@virginia.edu>
References: <CF8F3F39-4182-4BF0-BE5E-C162BAFF2E48@virginia.edu>
Message-ID: <200606120957.k5C9v3NE005121@idns103.gen-info.osaka-u.ac.jp>

Hi,

On Mon, 5 Jun 2006 14:00:56 -0400
Anoop Ranganath <ahr6y at virginia.edu> wrote:

> I'd like to add a simple flatfile format to use with bioruby.  In  
> particular, I'm looking at BED files, which have a very simple tab  
> delimited format.  I'm poking around in the code, and haven't been  
> able to find a good example of how to incorporate a new parser.  I'm  
> not so much interested in adding support for autodetection, so I  
> can't imagine that it would be too difficult.
> 
> Does anyone have a starting point I can use?
> 
> Thanks,
> Anoop 

If you are using bioruby-1.0.0, some critical bugs have been
found in the flatfile.rb. Please apply attached patch.

A very simple parser for tab separated values. It reads an entire file
at a time when initializing the parser class.
######################################################################
require 'bio'

# very simple parser for tab-separated data
class SimpleFormat
   # delimiter needed for flatfile
   DELIMITER = RS = nil # nil means no delimiter and reading entire file
   def initialize(str)
      @data = str.split(/\n/).collect { |x| x.to_s.split(/\t/) }
   end
   attr_reader :data
end

# example code to read a file 'test.dat' and show data
Bio::FlatFile.open(SimpleFormat, 'test.dat') do |ff|
   ff.each do |entry|
      p entry.data
   end
end
######################################################################

A simple example to parse a file with multiple entries, and
each end of the entry is '//'.
######################################################################
require 'bio'

# very simple parser for "//"-separated entries
class SimpleFormat2
   # delimiter needed for flatfile
   DELIMITER = RS = '//' # the end of each entry is '//'
   def initialize(str)
      # very simple parser only to store a text data
      @data = str
   end
   attr_reader :data
end

# example code to read a file 'sample.gbk' and shows each entry
Bio::FlatFile.open(SimpleFormat2, 'sample.gbk') do |ff|
   ff.each do |entry|
      p entry.data
   end
end
######################################################################

If you want to parse a data with variable delimiters or no explicit
delimiters, you need to write a splitter class to read an entry
from an IO wrapper object created by the FlatFile class.
However, the specifications of the splitter class haven't been
clearly determined yet, and will be changed in the near future.

In addition, the flatfile.rb is now under re-construction and
descriptions above might be changed.

-- 
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
Department of Genome Informatics, Genome Information Research Center,
Research Institute for Microbial Diseases, Osaka University, Japan

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From jan.aerts at bbsrc.ac.uk  Mon Jun  5 10:14:22 2006
From: jan.aerts at bbsrc.ac.uk (jan aerts (RI))
Date: Mon, 5 Jun 2006 11:14:22 +0100
Subject: [BioRuby] classes for chromosomes, genes, exons, polymorphisms, ...
Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DADA5@rie2ksrv1.ri.bbsrc.ac.uk>

All,

As far as I know, there are no classes that describe biological concepts
such as 'a chromosome', or 'a gene', or 'an exon'. I'm working out if I
need these things for my own purposes, but wonder if it would be
worthwhile to include them into bioruby? I was thinking of something
like:
  Bio::Entity::Chromosome
  Bio::Entity::Gene
  Bio::Entity::Exon
  Bio::Entity::Repeat
  Bio::Entity::Polymorphism
    Bio::Entity::SNP
    Bio::Entity::Microsatellite

I don't know if Bio::Entity::Chromosome would be necessary, because its
principal use would be to holds annotations (i.e. act as a map), so I
suppose that Bio::Map::SimpleMap could be instead...

Bio::Entity::Gene would include Bio::Map::ActsAsMarker and
Bio::Map::ActsLikeMap, so that a gene can be mapped to something like a
chromosome, but it can also have exons or polymorphisms mapped to it.

Worth to pursue this? And if so: any ideas/comments welcome...

Jan Aerts, PhD
Bioinformatics Group
Roslin Institute
Roslin, Scotland, UK
+44 131 527 4200

---------The obligatory disclaimer--------
The information contained in this e-mail (including any attachments) is
confidential and is intended for the use of the addressee only.   The
opinions expressed within this e-mail (including any attachments) are
the opinions of the sender and do not necessarily constitute those of
Roslin Institute (Edinburgh) ("the Institute") unless specifically
stated by a sender who is duly authorised to do so on behalf of the
Institute. 



From ahr6y at virginia.edu  Mon Jun  5 18:00:56 2006
From: ahr6y at virginia.edu (Anoop Ranganath)
Date: Mon, 5 Jun 2006 14:00:56 -0400
Subject: [BioRuby] adding a flatfile format
Message-ID: <CF8F3F39-4182-4BF0-BE5E-C162BAFF2E48@virginia.edu>

I'd like to add a simple flatfile format to use with bioruby.  In  
particular, I'm looking at BED files, which have a very simple tab  
delimited format.  I'm poking around in the code, and haven't been  
able to find a good example of how to incorporate a new parser.  I'm  
not so much interested in adding support for autodetection, so I  
can't imagine that it would be too difficult.

Does anyone have a starting point I can use?

Thanks,
Anoop 

From ngoto at gen-info.osaka-u.ac.jp  Mon Jun 12 09:56:58 2006
From: ngoto at gen-info.osaka-u.ac.jp (GOTO Naohisa)
Date: Mon, 12 Jun 2006 18:56:58 +0900
Subject: [BioRuby] adding a flatfile format
In-Reply-To: <CF8F3F39-4182-4BF0-BE5E-C162BAFF2E48@virginia.edu>
References: <CF8F3F39-4182-4BF0-BE5E-C162BAFF2E48@virginia.edu>
Message-ID: <200606120957.k5C9v3NE005121@idns103.gen-info.osaka-u.ac.jp>

Hi,

On Mon, 5 Jun 2006 14:00:56 -0400
Anoop Ranganath <ahr6y at virginia.edu> wrote:

> I'd like to add a simple flatfile format to use with bioruby.  In  
> particular, I'm looking at BED files, which have a very simple tab  
> delimited format.  I'm poking around in the code, and haven't been  
> able to find a good example of how to incorporate a new parser.  I'm  
> not so much interested in adding support for autodetection, so I  
> can't imagine that it would be too difficult.
> 
> Does anyone have a starting point I can use?
> 
> Thanks,
> Anoop 

If you are using bioruby-1.0.0, some critical bugs have been
found in the flatfile.rb. Please apply attached patch.

A very simple parser for tab separated values. It reads an entire file
at a time when initializing the parser class.
######################################################################
require 'bio'

# very simple parser for tab-separated data
class SimpleFormat
   # delimiter needed for flatfile
   DELIMITER = RS = nil # nil means no delimiter and reading entire file
   def initialize(str)
      @data = str.split(/\n/).collect { |x| x.to_s.split(/\t/) }
   end
   attr_reader :data
end

# example code to read a file 'test.dat' and show data
Bio::FlatFile.open(SimpleFormat, 'test.dat') do |ff|
   ff.each do |entry|
      p entry.data
   end
end
######################################################################

A simple example to parse a file with multiple entries, and
each end of the entry is '//'.
######################################################################
require 'bio'

# very simple parser for "//"-separated entries
class SimpleFormat2
   # delimiter needed for flatfile
   DELIMITER = RS = '//' # the end of each entry is '//'
   def initialize(str)
      # very simple parser only to store a text data
      @data = str
   end
   attr_reader :data
end

# example code to read a file 'sample.gbk' and shows each entry
Bio::FlatFile.open(SimpleFormat2, 'sample.gbk') do |ff|
   ff.each do |entry|
      p entry.data
   end
end
######################################################################

If you want to parse a data with variable delimiters or no explicit
delimiters, you need to write a splitter class to read an entry
from an IO wrapper object created by the FlatFile class.
However, the specifications of the splitter class haven't been
clearly determined yet, and will be changed in the near future.

In addition, the flatfile.rb is now under re-construction and
descriptions above might be changed.

-- 
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
Department of Genome Informatics, Genome Information Research Center,
Research Institute for Microbial Diseases, Osaka University, Japan

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