bio 1.3.1 → 1.4.0

data/sample/demo_blast_report.rb

@@ -0,0 +1,285 @@
+#
+# = sample/demo_blast_report.rb - demonstration of Bio::Blast::Report, Bio::Blast::Default::Report, and Bio::Blast::WU::Report
+# 
+# Copyright::  Copyright (C) 2003 Toshiaki Katayama <k@bioruby.org>
+# Copyright::  Copyright (C) 2003-2006,2008-2009 Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::Blast::Report (NCBI BLAST XML format parser),
+# Bio::Blast::Default::Report (NCBI BLAST default (-m 0) format parser),
+# and Bio::Blast::WU::Report (WU-BLAST default format parser).
+#
+# == Usage
+#
+# Specify files containing BLAST results.
+#
+#  $ ruby demo_blast_report.rb files...
+#
+# Example usage using test data:
+#
+#  $ ruby -Ilib sample/demo_blast_report.rb test/data/blast/b0002.faa.m7
+#  $ ruby -Ilib sample/demo_blast_report.rb test/data/blast/b0002.faa.m0
+#
+# == Development information
+#
+# The code was moved from lib/bio/appl/blast/report.rb,
+# lib/bio/appl/blast/format0.rb, and lib/bio/appl/blast/wublast.rb,
+# and modified.
+#
+
+require 'bio'
+
+# dummpy class to return specific object
+class Dummy
+  def initialize(obj)
+    @obj = obj
+  end
+  def size
+    @obj
+  end
+  def inspect
+    @obj.inspect
+  end
+end #class Dummy
+
+# wrapper class to ignore error
+class Wrapper
+  def initialize(obj)
+    @obj = obj
+  end
+  def class
+    @obj.class
+  end
+  def respond_to?(*arg)
+    @obj.respond_to?(*arg)
+  end
+  def method_missing(meth, *arg, &block)
+    begin
+      @obj.__send__(meth, *arg, &block)
+    rescue NoMethodError => evar
+      Dummy.new(evar)
+    end
+  end
+end #class Wrapper
+
+def wrap(obj)
+  Wrapper.new(obj)
+end
+
+# -m0: not defined in Bio::Blast::Default::Report ???
+# +m0: newly added in Bio::Blast::Default::Report ???
+# -WU: not defined in Bio::Blast::WU::Report ???
+# +WU: newly added in Bio::Blast::WU::Report ???
+
+Bio::FlatFile.open(ARGF) do |ff|
+  puts "Detected file format: #{ff.dbclass}"
+  unless ff.dbclass then
+    ff.dbclass = Bio::Blast::Report
+    puts "Input data may be tab-delimited format (-m 8)."
+  end
+  ff.each do |rep|
+  rep = wrap(rep)
+
+  #print "# === Bio::Blast::Default::Report\n"
+  print "# === #{rep.class}\n"
+  puts
+  print "  rep.program           #=> "; p rep.program
+  print "  rep.version           #=> "; p rep.version
+  print "  rep.reference         #=> "; p rep.reference
+  print "  rep.notice       [WU] #=> "; p rep.notice              #+WU
+  print "  rep.db                #=> "; p rep.db
+  print "  rep.query_id          #=> "; p rep.query_id        #-m0,-WU
+  print "  rep.query_def         #=> "; p rep.query_def
+  print "  rep.query_len         #=> "; p rep.query_len
+  #puts
+  print "  rep.version_number    #=> "; p rep.version_number  #+m0,+WU
+  print "  rep.version_date      #=> "; p rep.version_date    #+m0,+WU
+  puts
+
+  print "# === Parameters\n"
+  #puts
+  print "  rep.parameters        #=> "; p rep.parameters      #-m0
+  puts
+  print "  rep.matrix            #=> "; p rep.matrix              #-WU
+  print "  rep.expect            #=> "; p rep.expect
+  print "  rep.inclusion         #=> "; p rep.inclusion       #-m0,-WU
+  print "  rep.sc_match          #=> "; p rep.sc_match            #-WU
+  print "  rep.sc_mismatch       #=> "; p rep.sc_mismatch         #-WU
+  print "  rep.gap_open          #=> "; p rep.gap_open            #-WU
+  print "  rep.gap_extend        #=> "; p rep.gap_extend          #-WU
+  print "  rep.filter            #=> "; p rep.filter          #-m0,-WU
+  print "  rep.pattern           #=> "; p rep.pattern             #-WU
+  print "  rep.entrez_query      #=> "; p rep.entrez_query    #-m0
+  #puts
+  print "  rep.pattern_positions #=> "; p rep.pattern_positions #+m0
+  puts
+
+  print "# === Statistics (last iteration's)\n"
+  #puts
+  print "  rep.statistics        #=> "; p rep.statistics      #-m0,-WU
+  puts
+  print "  rep.db_num            #=> "; p rep.db_num
+  print "  rep.db_len            #=> "; p rep.db_len
+  print "  rep.hsp_len           #=> "; p rep.hsp_len         #-m0,-WU
+  print "  rep.eff_space         #=> "; p rep.eff_space           #-WU
+  print "  rep.kappa             #=> "; p rep.kappa               #-WU
+  print "  rep.lambda            #=> "; p rep.lambda              #-WU
+  print "  rep.entropy           #=> "; p rep.entropy             #-WU
+  puts
+  print "  rep.num_hits          #=> "; p rep.num_hits        #+m0
+  print "  rep.gapped_kappa      #=> "; p rep.gapped_kappa    #+m0
+  print "  rep.gapped_lambda     #=> "; p rep.gapped_lambda   #+m0
+  print "  rep.gapped_entropy    #=> "; p rep.gapped_entropy  #+m0
+  print "  rep.posted_date       #=> "; p rep.posted_date     #+m0
+  puts
+
+  print "# === Message (last iteration's)\n"
+  puts
+  print "  rep.message           #=> "; p rep.message             #-WU
+  #puts
+  print "  rep.converged?        #=> "; p rep.converged?      #+m0
+  puts
+
+  print "# === Warning messages\n"
+  print "  rep.warnings     [WU] #=> "; p rep.warnings            #+WU
+
+  print "# === Iterations\n"
+  puts
+  print "  rep.itrerations.each do |itr|\n"
+  puts
+
+  rep.iterations.each do |itr|
+  itr = wrap(itr)
+      
+  #print "# --- Bio::Blast::Default::Report::Iteration\n"
+  print "# --- #{itr.class}\n"
+  puts
+
+  print "    itr.num             #=> "; p itr.num
+  print "    itr.statistics      #=> "; p itr.statistics      #-m0,-WU
+  print "    itr.warnings   [WU] #=> "; p itr.warnings            #+WU
+  print "    itr.message         #=> "; p itr.message
+  print "    itr.hits.size       #=> "; p itr.hits.size
+  #puts
+  print "    itr.hits_newly_found.size    #=> "; p((itr.hits_newly_found.size rescue nil)); #+m0
+  print "    itr.hits_found_again.size    #=> "; p((itr.hits_found_again.size rescue nil)); #+m0
+  if itr.respond_to?(:hits_for_pattern) and itr.hits_for_pattern then #+m0
+  itr.hits_for_pattern.each_with_index do |hp, hpi|
+  print "    itr.hits_for_pattern[#{hpi}].size #=> "; p hp.size;
+  end
+  end
+  print "    itr.converged?      #=> "; p itr.converged?      #+m0,+WU
+  puts
+
+  print "    itr.hits.each do |hit|\n"
+  puts
+
+  itr.hits.each_with_index do |hit, i|
+  hit = wrap(hit)
+
+  #print "# --- Bio::Blast::Default::Report::Hit"
+  print "# --- #{hit.class}"
+  print " ([#{i}])\n"
+  puts
+
+  print "      hit.num           #=> "; p hit.num             #-m0,-WU
+  print "      hit.hit_id        #=> "; p hit.hit_id          #-m0,-WU
+  print "      hit.len           #=> "; p hit.len
+  print "      hit.definition    #=> "; p hit.definition
+  print "      hit.accession     #=> "; p hit.accession       #-m0,-WU
+  #puts
+  print "      hit.found_again?  #=> "; p hit.found_again?    #+m0,+WU
+  print "      hit.score    [WU] #=> "; p hit.score               #+WU
+  print "      hit.pvalue   [WU] #=> "; p hit.pvalue              #+WU
+  print "      hit.n_number [WU] #=> "; p hit.n_number            #+WU
+
+  print "        --- compatible/shortcut ---\n"
+  print "      hit.query_id      #=> "; p hit.query_id        #-m0,-WU
+  print "      hit.query_def     #=> "; p hit.query_def       #-m0,-WU
+  print "      hit.query_len     #=> "; p hit.query_len       #-m0,-WU
+  print "      hit.target_id     #=> "; p hit.target_id       #-m0,-WU
+  print "      hit.target_def    #=> "; p hit.target_def
+  print "      hit.target_len    #=> "; p hit.target_len
+
+  print "            --- first HSP's values (shortcut) ---\n"
+  print "      hit.evalue        #=> "; p hit.evalue
+  print "      hit.bit_score     #=> "; p hit.bit_score
+  print "      hit.identity      #=> "; p hit.identity
+  print "      hit.overlap       #=> "; p hit.overlap         #-m0,-WU
+
+  print "      hit.query_seq     #=> "; p hit.query_seq
+  print "      hit.midline       #=> "; p hit.midline
+  print "      hit.target_seq    #=> "; p hit.target_seq
+
+  print "      hit.query_start   #=> "; p hit.query_start
+  print "      hit.query_end     #=> "; p hit.query_end
+  print "      hit.target_start  #=> "; p hit.target_start
+  print "      hit.target_end    #=> "; p hit.target_end
+  print "      hit.lap_at        #=> "; p hit.lap_at
+  print "            --- first HSP's vaules (shortcut) ---\n"
+  print "        --- compatible/shortcut ---\n"
+
+  puts
+  print "      hit.hsps.size     #=> "; p hit.hsps.size
+  if hit.hsps.size == 0 then
+  puts  "          (HSP not found: please see blastall's -b and -v options)"
+  puts
+  else
+
+  puts
+  print "      hit.hsps.each do |hsp|\n"
+  puts
+
+  hit.hsps.each_with_index do |hsp, j|
+  hsp = wrap(hsp)
+
+  #print "# --- Bio::Blast::Default::Report::Hsp"
+  print "# --- #{hsp.class}"
+  print " ([#{j}])\n"
+  puts
+  print "        hsp.num         #=> "; p hsp.num             #-m0,-WU
+  print "        hsp.bit_score   #=> "; p hsp.bit_score 
+  print "        hsp.score       #=> "; p hsp.score
+  print "        hsp.evalue      #=> "; p hsp.evalue
+  print "        hsp.identity    #=> "; p hsp.identity
+  print "        hsp.gaps        #=> "; p hsp.gaps
+  print "        hsp.positive    #=> "; p hsp.positive
+  print "        hsp.align_len   #=> "; p hsp.align_len
+  print "        hsp.density     #=> "; p hsp.density         #-m0,-WU
+  print "        hsp.pvalue  [WU]#=> "; p hsp.pvalue              #+WU
+  print "        hsp.p_sum_n [WU]#=> "; p hsp.p_sum_n             #+WU
+
+  print "        hsp.query_frame #=> "; p hsp.query_frame
+  print "        hsp.query_from  #=> "; p hsp.query_from
+  print "        hsp.query_to    #=> "; p hsp.query_to
+
+  print "        hsp.hit_frame   #=> "; p hsp.hit_frame
+  print "        hsp.hit_from    #=> "; p hsp.hit_from
+  print "        hsp.hit_to      #=> "; p hsp.hit_to
+
+  print "        hsp.pattern_from#=> "; p hsp.pattern_from    #-m0,-WU
+  print "        hsp.pattern_to  #=> "; p hsp.pattern_to      #-m0,-WU
+
+  print "        hsp.qseq        #=> "; p hsp.qseq
+  print "        hsp.midline     #=> "; p hsp.midline
+  print "        hsp.hseq        #=> "; p hsp.hseq
+  puts
+  print "        hsp.percent_identity  #=> "; p hsp.percent_identity
+  print "        hsp.mismatch_count    #=> "; p hsp.mismatch_count   #-m0,-WU
+  #
+  print "        hsp.query_strand      #=> "; p hsp.query_strand     #+m0,+WU
+  print "        hsp.hit_strand        #=> "; p hsp.hit_strand       #+m0,+WU
+  print "        hsp.percent_positive  #=> "; p hsp.percent_positive #+m0,+WU
+  print "        hsp.percent_gaps      #=> "; p hsp.percent_gaps     #+m0,+WU
+  puts
+
+  end #each
+  end #if hit.hsps.size == 0
+  end
+  end
+  end #ff.each
+end #Bio::FlatFile.open
+

data/sample/demo_codontable.rb

@@ -0,0 +1,119 @@
+#
+# = sample/demo_codontable.rb - demonstration of Bio::CodonTable
+#
+# Copyright::	Copyright (C) 2001, 2004
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::CodonTable.
+#
+# == Usage
+#
+# Simply run this script.
+#
+#  $ ruby demo_codontable.rb
+#
+# == Development information
+#
+# The code was moved from lib/bio/data/codontable.rb.
+#
+
+require 'bio'
+
+
+#if __FILE__ == $0
+
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  puts "### Bio::CodonTable[1]"
+  p ct1 = Bio::CodonTable[1]
+
+  puts ">>> Bio::CodonTable#table"
+  p ct1.table
+
+  puts ">>> Bio::CodonTable#each"
+  ct1.each do |codon, aa|
+    puts "#{codon} -- #{aa}"
+  end
+
+  puts ">>> Bio::CodonTable#definition"
+  p ct1.definition
+
+  puts ">>> Bio::CodonTable#['atg']"
+  p ct1['atg']
+
+  puts ">>> Bio::CodonTable#revtrans('A')"
+  p ct1.revtrans('A')
+
+  puts ">>> Bio::CodonTable#start_codon?('atg')"
+  p ct1.start_codon?('atg')
+  
+  puts ">>> Bio::CodonTable#start_codon?('aaa')"
+  p ct1.start_codon?('aaa')
+
+  puts ">>> Bio::CodonTable#stop_codon?('tag')"
+  p ct1.stop_codon?('tag')
+  
+  puts ">>> Bio::CodonTable#stop_codon?('aaa')"
+  p ct1.stop_codon?('aaa')
+
+  puts ">>> ct1_copy = Bio::CodonTable.copy(1)"
+  p ct1_copy = Bio::CodonTable.copy(1)
+  puts ">>> ct1_copy['tga'] = 'U'"
+  p ct1_copy['tga'] = 'U'
+  puts " orig : #{ct1['tga']}"
+  puts " copy : #{ct1_copy['tga']}"
+
+
+  puts "### ct = Bio::CodonTable.new(hash, definition)"
+  hash = {
+    'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
+    'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
+    'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'U',
+    'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
+
+    'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
+    'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
+    'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
+    'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
+
+    'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
+    'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
+    'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
+    'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
+
+    'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
+    'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
+    'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
+    'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
+  }
+  my_ct = Bio::CodonTable.new(hash, "my codon table")
+
+  puts ">>> ct.definition"
+  puts my_ct.definition
+
+  puts ">>> ct.definition=(str)"
+  my_ct.definition = "selenoproteins (Eukaryote)"
+  puts my_ct.definition
+
+  puts ">>> ct['tga']"
+  puts my_ct['tga']
+
+  puts ">>> ct.revtrans('U')"
+  puts my_ct.revtrans('U')
+
+  puts ">>> ct.stop_codon?('tga')"
+  puts my_ct.stop_codon?('tga')
+
+  puts ">>> ct.stop_codon?('tag')"
+  puts my_ct.stop_codon?('tag')
+
+#end
+

data/sample/demo_das.rb

@@ -0,0 +1,105 @@
+#
+# = sample/demo_go.rb - demonstration of Bio::DAS, BioDAS access module
+#
+# Copyright::	Copyright (C) 2003, 2004, 2007
+#		Shuichi Kawashima <shuichi@hgc.jp>,
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	The Ruby License
+#
+#
+# == Description
+#
+# Demonstration of Bio::GO, BioDAS access module.
+#
+# == Requirements
+#
+# Internet connection is needed.
+#
+# == Usage
+#
+# Simply run this script.
+#
+#  $ ruby demo_das.rb
+#
+# == Notes
+#
+# Demo using the WormBase DAS server is temporarily disabled because
+# it does not work well possibly because of the server trouble.
+#
+# == Development information
+#
+# The code was moved from lib/bio/io/das.rb and modified as below:
+#
+# * Demo codes using UCSC DAS server is added.
+#
+
+require 'bio'
+
+# begin
+#   require 'pp'
+#   alias p pp
+# rescue LoadError
+# end
+
+if false #disabled
+  puts "### WormBase"
+  wormbase = Bio::DAS.new('http://www.wormbase.org/db/')
+
+  puts ">>> test get_dsn"
+  p wormbase.get_dsn
+
+  puts ">>> create segment obj Bio::DAS::SEGMENT.region('I', 1, 1000)"
+  seg = Bio::DAS::SEGMENT.region('I', 1, 1000)
+  p seg
+
+  puts ">>> test get_dna"
+  p wormbase.get_dna('elegans', seg)
+
+  puts "### test get_features"
+  p wormbase.get_features('elegans', seg)
+end #if false #disabled
+
+if true #enabled
+  puts "### UCSC"
+  ucsc = Bio::DAS.new('http://genome.ucsc.edu/cgi-bin/')
+
+  puts ">>> test get_dsn"
+  p ucsc.get_dsn
+
+  puts ">>> test get_entry_points('hg19')"
+  p ucsc.get_entry_points('hg19')
+
+  puts ">>> test get_types('hg19')"
+  p ucsc.get_types('hg19')
+
+  len = rand(50) * 10 + 100
+  pos = rand(243199373 - len)
+  puts ">>> create segment obj Bio::DAS::SEGMENT.region('2', #{pos}, #{pos + len - 1})"
+  seg2 = Bio::DAS::SEGMENT.region('2', pos, pos + len - 1)
+  p seg2
+
+  puts ">>> test get_dna"
+  p ucsc.get_dna('hg19', seg2)
+
+  puts "### test get_features"
+  p ucsc.get_features('hg19', seg2)
+end #if true #enabled
+
+if true #enabled
+  puts "### KEGG DAS"
+  kegg_das = Bio::DAS.new("http://das.hgc.jp/cgi-bin/")
+
+  dsn_list = kegg_das.get_dsn
+  org_list = dsn_list.collect {|x| x.source}
+
+  puts ">>> dsn : entry_points"
+  org_list.each do |org|
+    print "#{org} : "
+    list = kegg_das.get_entry_points(org)
+    list.segments.each do |seg|
+      print " #{seg.entry_id}"
+    end
+    puts
+  end
+end #if true #enabled
+