bio 1.3.1 → 1.4.0

data/sample/demo_kegg_compound.rb

@@ -0,0 +1,57 @@
+#
+# = sample/demo_kegg_compound.rb - demonstration of Bio::KEGG::COMPOUND
+#
+# Copyright::  Copyright (C) 2001, 2002, 2004, 2007 Toshiaki Katayama <k@bioruby.org>
+# Copyright::  Copyright (C) 2009 Kozo Nishida <kozo-ni@is.naist.jp>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::KEGG::COMPOUND, a parser class for the KEGG COMPOUND
+# chemical structure database.
+#
+# == Usage
+#
+# Specify files containing KEGG COMPOUND data.
+#
+#  $ ruby demo_kegg_compound.rb files...
+#
+# Example usage using test data:
+#
+#  $ ruby -Ilib sample/demo_kegg_compound.rb test/data/KEGG/C00025.compound
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/kegg/compound.rb and modified.
+#
+
+require 'bio'
+
+Bio::FlatFile.foreach(Bio::KEGG::COMPOUND, ARGF) do |cpd|
+  puts "### cpd = Bio::KEGG::COMPOUND.new(str)"
+  puts "# cpd.entry_id"
+  p cpd.entry_id
+  puts "# cpd.names"
+  p cpd.names
+  puts "# cpd.name"
+  p cpd.name
+  puts "# cpd.formula"
+  p cpd.formula
+  puts "# cpd.mass"
+  p cpd.mass
+  puts "# cpd.reactions"
+  p cpd.reactions
+  puts "# cpd.rpairs"
+  p cpd.rpairs
+  puts "# cpd.pathways"
+  p cpd.pathways
+  puts "# cpd.enzymes"
+  p cpd.enzymes
+  puts "# cpd.dblinks"
+  p cpd.dblinks
+  puts "# cpd.kcf"
+  p cpd.kcf
+  puts "=" * 78
+end
+

data/sample/demo_kegg_drug.rb

@@ -0,0 +1,65 @@
+#
+# = sample/demo_kegg_drug.rb - demonstration of Bio::KEGG::DRUG
+#
+# Copyright::  Copyright (C) 2007 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::KEGG::DRUG, a parser class for the KEGG DRUG
+# drug database entry.
+#
+# == Usage
+#
+# Specify files containing KEGG DRUG data.
+#
+#  $ ruby demo_kegg_drug.rb files...
+#
+# == Example of running this script
+#
+# Download test data.
+#
+#  $ ruby -Ilib bin/br_biofetch.rb dr D00001 > D00001.drug
+#  $ ruby -Ilib bin/br_biofetch.rb dr D00002 > D00002.drug
+#
+# Run this script.
+#
+#  $ ruby -Ilib sample/demo_kegg_drug.rb D00001.drug D00002.drug
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/kegg/drug.rb and modified.
+#
+
+require 'bio'
+
+Bio::FlatFile.foreach(Bio::KEGG::DRUG, ARGF) do |dr|
+  #entry = ARGF.read	# dr:D00001
+  #dr = Bio::KEGG::DRUG.new(entry)
+
+  puts "### dr = Bio::KEGG::DRUG.new(str)"
+  puts "# dr.entry_id"
+  p dr.entry_id
+  puts "# dr.names"
+  p dr.names
+  puts "# dr.name"
+  p dr.name
+  puts "# dr.formula"
+  p dr.formula
+  puts "# dr.mass"
+  p dr.mass
+  puts "# dr.activity"
+  p dr.activity
+  puts "# dr.remark"
+  p dr.remark
+  puts "# dr.comment"
+  p dr.comment
+  puts "# dr.dblinks"
+  p dr.dblinks
+  puts "# dr.kcf"
+  p dr.kcf
+
+  puts "=" * 78
+end
+

data/sample/demo_kegg_genome.rb

@@ -0,0 +1,74 @@
+#
+# = sample/demo_kegg_genome.rb - demonstration of Bio::KEGG::GENOME
+#
+# Copyright::  Copyright (C) 2001, 2002, 2007 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::KEGG::GENOME, a parser class for the KEGG/GENOME
+# genome database.
+#
+# == Usage
+#
+# Specify files containing KEGG GENOME data.
+#
+#  $ ruby demo_kegg_genome.rb files...
+#
+# == Example of running this script
+#
+# Download test data.
+#
+#  $ ruby -Ilib bin/br_biofetch.rb genome eco > eco.genome
+#  $ ruby -Ilib bin/br_biofetch.rb genome hsa > hsa.genome
+#
+# Run this script.
+#
+#  $ ruby -Ilib sample/demo_kegg_genome.rb eco.genome hsa.genome
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/kegg/genome.rb and modified.
+#
+
+require 'bio'
+
+#if __FILE__ == $0
+
+  begin
+    require 'pp'
+    def p(arg); pp(arg); end
+  rescue LoadError
+  end
+
+  #require 'bio/io/flatfile'
+
+  ff = Bio::FlatFile.new(Bio::KEGG::GENOME, ARGF)
+
+  ff.each do |genome|
+
+    puts "### Tags"
+    p genome.tags
+
+    [
+      %w( ENTRY entry_id ),
+      %w( NAME name ),
+      %w( DEFINITION definition ),
+      %w( TAXONOMY taxonomy taxid lineage ),
+      %w( REFERENCE references ),
+      %w( CHROMOSOME chromosomes ),
+      %w( PLASMID plasmids ),
+      %w( STATISTICS statistics nalen num_gene num_rna ),
+    ].each do |x|
+      puts "### " + x.shift
+      x.each do |m|
+        p genome.__send__(m)
+      end
+    end
+
+    puts "=" * 78
+  end
+
+#end
+

data/sample/demo_kegg_glycan.rb

@@ -0,0 +1,72 @@
+#
+# = sample/demo_kegg_glycan.rb - demonstration of Bio::KEGG::GLYCAN
+#
+# Copyright::  Copyright (C) 2004 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::KEGG::GLYCAN, a parser class for the KEGG GLYCAN
+# glycome informatics database.
+#
+# == Usage
+#
+# Specify files containing KEGG GLYCAN data.
+#
+#  $ ruby demo_kegg_glycan.rb files...
+#
+# == Example of running this script
+#
+# Download test data.
+#
+#  $ ruby -Ilib bin/br_biofetch.rb glycan G00001 > G00001.glycan
+#  $ ruby -Ilib bin/br_biofetch.rb glycan G00024 > G00024.glycan
+#
+# Run this script.
+#
+#  $ ruby -Ilib sample/demo_kegg_glycan.rb G00001.glycan G00024.glycan
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/kegg/glycan.rb and modified.
+#
+
+require 'bio'
+
+Bio::FlatFile.foreach(Bio::KEGG::GLYCAN, ARGF) do |gl|
+  #entry = ARGF.read	# gl:G00024
+  #gl = Bio::KEGG::GLYCAN.new(entry)
+
+  puts "### gl = Bio::KEGG::GLYCAN.new(str)"
+  puts "# gl.entry_id"
+  p gl.entry_id
+  puts "# gl.name"
+  p gl.name
+  puts "# gl.composition"
+  p gl.composition
+  puts "# gl.mass"
+  p gl.mass
+  puts "# gl.keggclass"
+  p gl.keggclass
+  #puts "# gl.bindings"
+  #p gl.bindings
+  puts "# gl.compounds"
+  p gl.compounds
+  puts "# gl.reactions"
+  p gl.reactions
+  puts "# gl.pathways"
+  p gl.pathways
+  puts "# gl.enzymes"
+  p gl.enzymes
+  puts "# gl.orthologs"
+  p gl.orthologs
+  puts "# gl.references"
+  p gl.references
+  puts "# gl.dblinks"
+  p gl.dblinks
+  puts "# gl.kcf"
+  p gl.kcf
+
+  puts "=" * 78
+end

data/sample/demo_kegg_orthology.rb

@@ -0,0 +1,62 @@
+#
+# = sample/demo_kegg_orthology.rb - demonstration of Bio::KEGG::ORTHOLOGY
+#
+# Copyright::  Copyright (C) 2003-2007 Toshiaki Katayama <k@bioruby.org>
+# Copyright::  Copyright (C) 2003 Masumi Itoh <m@bioruby.org>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::KEGG::ORTHOLOGY, the parser class for the KEGG
+# ORTHOLOGY database entry.
+#
+# == Usage
+#
+# Specify files containing KEGG ORTHOLOGY data.
+#
+#  $ ruby demo_kegg_orthology.rb files...
+#
+# == Example of running this script
+#
+# Download test data.
+#
+#  $ ruby -Ilib bin/br_biofetch.rb ko K00001 > K00001.ko
+#  $ ruby -Ilib bin/br_biofetch.rb ko K00161 > K00161.ko
+#
+# Run this script.
+#
+#  $ ruby -Ilib sample/demo_kegg_orthology.rb K00001.ko K00161.ko
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/kegg/orthology.rb and modified.
+#
+
+require 'bio'
+
+Bio::FlatFile.foreach(Bio::KEGG::ORTHOLOGY, ARGF) do |ko|
+  puts "### ko = Bio::KEGG::ORTHOLOGY.new(str)"
+
+  puts "# ko.ko_id"
+  p ko.entry_id
+  puts "# ko.name"
+  p ko.name
+  puts "# ko.names"
+  p ko.names
+  puts "# ko.definition"
+  p ko.definition
+  puts "# ko.keggclass"
+  p ko.keggclass
+  puts "# ko.keggclasses"
+  p ko.keggclasses
+  puts "# ko.pathways"
+  p ko.pathways
+  puts "# ko.dblinks"
+  p ko.dblinks
+  puts "# ko.genes"
+  p ko.genes
+
+  puts "=" * 78
+end
+

data/sample/demo_kegg_reaction.rb

@@ -0,0 +1,66 @@
+#
+# = sample/demo_kegg_reaction.rb - demonstration of Bio::KEGG::REACTION
+#
+# Copyright::  Copyright (C) 2004 Toshiaki Katayama <k@bioruby.org>
+# Copyright::  Copyright (C) 2009 Kozo Nishida <kozo-ni@is.naist.jp>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::KEGG::REACTION, the parser class for the KEGG
+# REACTION biochemical reaction database.
+#
+# == Usage
+#
+# Specify files containing KEGG REACTION data.
+#
+#  $ ruby demo_kegg_reaction.rb files...
+#
+# Example usage using test data:
+#
+#  $ ruby -Ilib sample/demo_kegg_reaction.rb test/data/KEGG/R00006.reaction 
+#
+# == Example of running this script
+#
+# Download test data.
+#
+#  $ ruby -Ilib bin/br_biofetch.rb reaction R00259 > R00259.reaction
+#  $ ruby -Ilib bin/br_biofetch.rb reaction R02282 > R02282.reaction
+#
+# Run this script.
+#
+#  $ ruby -Ilib sample/demo_kegg_reaction.rb R00259.reaction R02282.reaction
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/kegg/reaction.rb and modified.
+#
+
+require 'bio'
+
+Bio::FlatFile.foreach(Bio::KEGG::REACTION, ARGF) do |rn|
+  puts "### rn = Bio::KEGG::REACTION.new(str)"
+
+  puts "# rn.entry_id"
+  p rn.entry_id
+  puts "# rn.name"
+  p rn.name
+  puts "# rn.definition"
+  p rn.definition
+  puts "# rn.equation"
+  p rn.equation
+  puts "# rn.rpairs"
+  p rn.rpairs
+  puts "# rn.pathways"
+  p rn.pathways
+  puts "# rn.enzymes"
+  p rn.enzymes
+  puts "# rn.orthologs"
+  p rn.orthologs
+  puts "# rn.orthologs_as_hash"
+  p rn.orthologs_as_hash
+
+  puts "=" * 78
+end
+

data/sample/demo_kegg_taxonomy.rb

@@ -0,0 +1,92 @@
+#
+# = sample/demo_kegg_taxonomy.rb - demonstration of Bio::KEGG::Taxonomy
+#
+# Copyright::  Copyright (C) 2007 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# IMPORTANT NOTE: currently, this sample does not work!
+#
+# Demonstration of Bio::KEGG::Taxonomy.
+#
+# == Usage
+#
+# Specify a file containing KEGG Taxonomy data.
+#
+#  $ ruby demo_kegg_taxonomy.rb file
+#
+# Optionally, when a file containing organisms list (1 line per 1 organism)
+# is specified after the file, only the specified organisms are shown.
+#
+#  $ ruby demo_kegg_taxonomy.rb kegg_taxonomy_file org_list_file
+#
+# == Example of running this script
+#
+# Download test data.
+#
+#  $ wget ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
+#
+# The downloaded filename is "taxonomy".
+#
+# Run this script.
+#
+#  $ ruby -Ilib sample/demo_kegg_taxonomy.rb taxonomy
+#
+# == Development information
+#
+# The code was moved from lib/bio/db/kegg/taxonomy.rb.
+#
+
+require 'bio'
+
+#if __FILE__ == $0
+
+  # Usage:
+  # % wget ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
+  # % ruby taxonomy.rb taxonomy | less -S
+
+  taxonomy = ARGV.shift
+  org_list = ARGV.shift || nil
+
+  if org_list
+    orgs = File.readlines(org_list).map{|x| x.strip}
+  else
+    orgs = nil
+  end
+
+  tree = Bio::KEGG::Taxonomy.new(taxonomy, orgs)
+
+  puts ">>> tree - original"
+  puts tree
+
+  puts ">>> tree - after compact"
+  tree.compact
+  puts tree
+
+  puts ">>> tree - after reduce"
+  tree.reduce
+  puts tree
+
+  puts ">>> path - sorted"
+  tree.path.sort.each do |path|
+    puts path.join("/")
+  end
+
+  puts ">>> group : orgs"
+  tree.dfs(tree.root) do |parent, children|
+    if orgs = tree.organisms(parent)
+      puts "#{parent.ljust(30)} (#{orgs.size})\t#{orgs.join(', ')}"
+    end
+  end
+
+  puts ">>> group : subgroups"
+  tree.dfs_with_level(tree.root) do |parent, children, level|
+    subgroups = children.keys.sort
+    indent = " " * level
+    label  = "#{indent} #{level} #{parent}"
+    puts "#{label.ljust(35)}\t#{subgroups.join(', ')}"
+  end
+
+#end