bio 1.3.1 → 1.4.0

data/lib/bio/io/flatfile.rb

@@ -5,7 +5,7 @@
 #
 # License:: The Ruby License
 #
-#  $Id: flatfile.rb,v 1.61 2007/11/15 07:07:16 k Exp $
+#  $Id:$
 #
 #
 # Bio::FlatFile is a helper and wrapper class to read a biological data file.
@@ -465,9 +465,3 @@ module Bio
 
 end #module Bio
 
-if __FILE__ == $0
-  if ARGV.size == 2
-    require 'bio'
-    p Bio::FlatFile.open(eval(ARGV.shift), ARGV.shift).next_entry
-  end
-end

data/lib/bio/io/flatfile/autodetection.rb

@@ -477,6 +477,9 @@ module Bio
           sim4   = RuleRegexp[ 'Bio::Sim4::Report',
             /^seq1 \= .*\, \d+ bp(\r|\r?\n)seq2 \= .*\, \d+ bp(\r|\r?\n)/ ],
 
+          fastq  = RuleRegexp[ 'Bio::Fastq',
+            /^\@.+(?:\r|\r?\n)(?:[^\@\+].*(?:\r|\r?\n))+\+.*(?:\r|\r?\n).+(?:\r|\r?\n)/ ],
+
           fastaformat = RuleProc.new('Bio::FastaFormat',
                                      'Bio::NBRF',
                                      'Bio::FastaNumericFormat') do |text|
@@ -521,6 +524,9 @@ module Bio
         wublast.is_prior_to wutblast
         wutblast.is_prior_to blast
         blast.is_prior_to tblast
+        # Fastq
+        BottomRule.is_prior_to(fastq)
+        fastq.is_prior_to(fastaformat)
         # FastaFormat
         BottomRule.is_prior_to(fastaformat)
 

data/lib/bio/io/keggapi.rb

@@ -361,445 +361,3 @@ end # API
 end # KEGG
 end # Bio
 
-
-if __FILE__ == $0
-
-  begin
-    require 'pp'
-    alias p pp
-  rescue LoadError
-  end
-
-  puts ">>> KEGG API"
-  serv = Bio::KEGG::API.new
-# serv.log = STDERR
-
-  puts "# * parameters"
-  puts "        wsdl : #{serv.wsdl}"
-  puts "         log : #{serv.log}"
-  puts "       start : #{serv.start}"
-  puts " max_results : #{serv.max_results}"
-
-  puts "=== META"
-
-  puts "### list_databases"
-  list = serv.list_databases
-  list.each do |db|
-    print db.entry_id, "\t", db.definition, "\n"
-  end
-
-  puts "### list_organisms"
-  list = serv.list_organisms
-  list.each do |org|
-    print org.entry_id, "\t", org.definition, "\n"
-  end
-
-  puts "### list_pathways('map') : reference pathway"
-  list = serv.list_pathways("map")
-  list.each do |path|
-    print path.entry_id, "\t", path.definition, "\n"
-  end
-
-  puts "### list_pathways('eco') : E. coli pathway"
-  list = serv.list_pathways("eco")
-  list.each do |path|
-    print path.entry_id, "\t", path.definition, "\n"
-  end
-
-  puts "=== DBGET"
-
-  puts "### binfo('all')"
-  puts serv.binfo("all")
-
-  puts "### binfo('genbank')"
-  puts serv.binfo("genbank")
-
-  puts "### bfind('genbank kinase cell cycle human')"
-  puts serv.bfind("genbank kinase cell cycle human")
-
-  puts "### bget('gb:AJ617376')"
-  puts serv.bget("gb:AJ617376")
-
-  puts "### bget('eco:b0002 eco:b0003')"
-  puts serv.bget("eco:b0002 eco:b0003")
-
-  puts "### btit('eco:b0002 eco:b0003')"
-  puts serv.btit("eco:b0002 eco:b0003")
-
-  puts "# * get_entries(['eco:b0002', 'eco:b0003'])"
-  puts serv.get_entries(["eco:b0002", "eco:b0003"])
-
-  puts "# * get_aaseqs(['eco:b0002', 'eco:b0003'])"
-  puts serv.get_aaseqs(["eco:b0002", "eco:b0003"])
-
-  puts "# * get_naseqs(['eco:b0002', 'eco:b0003'])"
-  puts serv.get_naseqs(["eco:b0002", "eco:b0003"])
-
-  puts "# * get_definitions(['eco:b0002', 'eco:b0003'])"
-  puts serv.get_definitions(["eco:b0002", "eco:b0003"])
-
-  puts "# * get_definitions(('eco:b0001'..'eco:b0200').to_a)"
-  puts serv.get_definitions(("eco:b0001".."eco:b0200").to_a)
-
-  puts "=== LinkDB"
-
-  puts "### get_linkdb_by_entry('eco:b0002', 'pathway', 1, 5)"
-  list = serv.get_linkdb_by_entry("eco:b0002", "pathway", 1, 5)
-  list.each do |link|
-    puts [ link.entry_id1, link.entry_id2, link.type, link.path ].join("\t")
-  end
-
-  puts "# * get_all_linkdb_by_entry('eco:b0002', 'pathway')"
-  list = serv.get_all_linkdb_by_entry("eco:b0002", "pathway")
-  list.each do |link|
-    puts [ link.entry_id1, link.entry_id2, link.type, link.path ].join("\t")
-  end
-
-  puts "=== SSDB"
-
-  puts "### get_neighbors_by_gene('eco:b0002', 'all', 1, 5)"
-  list = serv.get_neighbors_by_gene("eco:b0002", "all", 1, 5)
-  list.each do |hit|
-    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
-  end
-
-  puts "# * get_all_neighbors_by_gene('eco:b0002', 'bsu')"
-  list = serv.get_all_neighbors_by_gene("eco:b0002", "bsu")
-  list.each do |hit|
-    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
-  end
-
-  puts "### get_best_best_neighbors_by_gene('eco:b0002', 1, 5)"
-  list = serv.get_best_best_neighbors_by_gene("eco:b0002", 1, 5)
-  list.each do |hit|
-    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
-  end
-
-  puts "# * get_all_best_best_neighbors_by_gene('eco:b0002')"
-  list = serv.get_all_best_best_neighbors_by_gene("eco:b0002")
-  list.each do |hit|
-    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
-  end
-
-  puts "### get_best_neighbors_by_gene('eco:b0002', 1, 5)"
-  list = serv.get_best_neighbors_by_gene("eco:b0002", 1, 5)
-  list.each do |hit|
-    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
-  end
-
-  puts "# * get_all_best_neighbors_by_gene('eco:b0002')"
-  list = serv.get_all_best_neighbors_by_gene("eco:b0002")
-  list.each do |hit|
-    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
-  end
-
-  puts "### get_reverse_best_neighbors_by_gene('eco:b0002', 1, 5)"
-  list = serv.get_reverse_best_neighbors_by_gene("eco:b0002", 1, 5)
-  list.each do |hit|
-    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
-  end
-
-  puts "# * get_all_reverse_best_neighbors_by_gene('eco:b0002')"
-  list = serv.get_all_reverse_best_neighbors_by_gene("eco:b0002")
-  list.each do |hit|
-    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
-  end
-
-  puts "### get_paralogs_by_gene('eco:b0002', 1, 5)"
-  list = serv.get_paralogs_by_gene("eco:b0002", 1, 5)
-  list.each do |hit|
-    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
-  end
-
-  puts "# * get_all_paralogs_by_gene('eco:b0002')"
-  list = serv.get_all_paralogs_by_gene("eco:b0002")
-  list.each do |hit|
-    puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
-  end
-
-  puts "### get_similarity_between_genes('eco:b0002', 'bsu:BG10350')"
-  relation = serv.get_similarity_between_genes("eco:b0002", "bsu:BG10350")
-  puts "        genes_id1 : #{relation.genes_id1}"		# string
-  puts "        genes_id2 : #{relation.genes_id2}"		# string
-  puts "         sw_score : #{relation.sw_score}"		# int
-  puts "        bit_score : #{relation.bit_score}"		# float
-  puts "         identity : #{relation.identity}"		# float
-  puts "          overlap : #{relation.overlap}"		# int
-  puts "  start_position1 : #{relation.start_position1}"	# int
-  puts "    end_position1 : #{relation.end_position1}"		# int
-  puts "  start_position2 : #{relation.start_position2}"	# int
-  puts "    end_position2 : #{relation.end_position2}"		# int
-  puts "   best_flag_1to2 : #{relation.best_flag_1to2}"		# boolean
-  puts "   best_flag_2to1 : #{relation.best_flag_2to1}"		# boolean
-  puts "      definition1 : #{relation.definition1}"		# string
-  puts "      definition2 : #{relation.definition2}"		# string
-  puts "          length1 : #{relation.length1}"		# int
-  puts "          length2 : #{relation.length2}"		# int
-
-  puts "=== MOTIF"
-
-  puts "### get_motifs_by_gene('eco:b0002', 'pfam')"
-  list = serv.get_motifs_by_gene("eco:b0002", "pfam")
-  list.each do |motif|
-    puts motif.motif_id
-  end if list
-
-  puts "### get_motifs_by_gene('eco:b0002', 'tfam')"
-  list = serv.get_motifs_by_gene("eco:b0002", "tfam")
-  list.each do |motif|
-    puts motif.motif_id
-  end if list
-
-  puts "### get_motifs_by_gene('eco:b0002', 'pspt')"
-  list = serv.get_motifs_by_gene("eco:b0002", "pspt")
-  list.each do |motif|
-    puts motif.motif_id
-  end if list
-
-  puts "### get_motifs_by_gene('eco:b0002', 'pspf')"
-  list = serv.get_motifs_by_gene("eco:b0002", "pspf")
-  list.each do |motif|
-    puts motif.motif_id
-  end if list
-
-  puts "### get_motifs_by_gene('eco:b0002', 'all')"
-  list = serv.get_motifs_by_gene("eco:b0002", "all")
-  list.each do |motif|
-    puts "# * motif result"
-    puts "       motif_id : #{motif.motif_id}"
-    puts "     definition : #{motif.definition}"
-    puts "       genes_id : #{motif.genes_id}"
-    puts " start_position : #{motif.start_position}"
-    puts "   end_position : #{motif.end_position}"
-    puts "          score : #{motif.score}"
-    puts "         evalue : #{motif.evalue}"
-  end
-
-  puts "### get_genes_by_motifs(['pf:ACT', 'ps:ASPARTOKINASE'], 1, 5)"
-  list = serv.get_genes_by_motifs(["pf:ACT", "ps:ASPARTOKINASE"], 1, 5)
-  list.each do |gene|
-    puts [ gene.entry_id, gene.definition ].join("\t")
-  end
-
-  puts "# * get_all_genes_by_motifs(['pf:ACT', 'ps:ASPARTOKINASE'])"
-  list = serv.get_all_genes_by_motifs(["pf:ACT", "ps:ASPARTOKINASE"])
-  list.each do |gene|
-    puts [ gene.entry_id, gene.definition ].join("\t")
-  end
-
-  puts "=== KO, OC, PC"
-
-  puts "### get_ko_by_gene('eco:b0002')"
-  list = serv.get_ko_by_gene("eco:b0002")
-  list.each do |ko|
-    puts ko
-  end
-
-  puts "### get_ko_members('ko:K00003')"
-  list = serv.get_ko_members("ko:K00003")
-  list.each do |gene|
-    puts gene
-  end
-
-  puts "### get_oc_members_by_gene('eco:b0002', 1, 5)"
-  list = serv.get_oc_members_by_gene("eco:b0002", 1, 5)
-  list.each do |gene|
-    puts gene
-  end
-
-  puts "# * get_all_oc_members_by_gene('eco:b0002')"
-  list = serv.get_all_oc_members_by_gene("eco:b0002")
-  list.each do |gene|
-    puts gene
-  end
-
-  puts "### get_pc_members_by_gene('eco:b0002', 1, 5)"
-  list = serv.get_pc_members_by_gene("eco:b0002", 1, 5)
-  list.each do |gene|
-    puts gene
-  end
-
-  puts "# * get_all_pc_members_by_gene('eco:b0002')"
-  list = serv.get_all_pc_members_by_gene("eco:b0002")
-  list.each do |gene|
-    puts gene
-  end
-
-  puts "=== PATHWAY"
-
-  puts "==== coloring pathway"
-
-  puts "### mark_pathway_by_objects('path:eco00260', obj_list)"
-  puts "  obj_list = ['eco:b0002', 'cpd:C00263']"
-  obj_list = ["eco:b0002", "cpd:C00263"]
-  url = serv.mark_pathway_by_objects("path:eco00260", obj_list)
-  puts url
-
-  puts "### color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)"
-  puts "  obj_list = ['eco:b0207', 'eco:b1300']"
-  puts "  fg_list  = ['blue', '#00ff00']"
-  puts "  bg_list  = ['#ff0000', 'yellow']"
-  obj_list = ["eco:b0207", "eco:b1300"]
-  fg_list  = ["blue", "#00ff00"]
-  bg_list  = ["#ff0000", "yellow"]
-  url = serv.color_pathway_by_objects("path:eco00053", obj_list, fg_list, bg_list)
-  puts url
-
-  #puts "# * save_image(#{url})"
-  #filename = serv.save_image(url, "test.gif")
-  #filename = serv.save_image(url)
-  #puts filename
-
-  puts "==== objects on pathway"
-
-  puts "### get_genes_by_pathway('path:map00010')"
-  list = serv.get_genes_by_pathway("path:map00010")
-  list.each do |gene|
-    puts gene
-  end
-
-  puts "### get_genes_by_pathway('path:eco00010')"
-  list = serv.get_genes_by_pathway("path:eco00010")
-  list.each do |gene|
-    puts gene
-  end
-
-  puts "### get_enzymes_by_pathway('path:map00010')"
-  list = serv.get_enzymes_by_pathway("path:map00010")
-  list.each do |enzyme|
-    puts enzyme
-  end
-
-  puts "### get_enzymes_by_pathway('path:eco00010')"
-  list = serv.get_enzymes_by_pathway("path:eco00010")
-  list.each do |enzyme|
-    puts enzyme
-  end
-
-  puts "### get_compounds_by_pathway('path:map00010')"
-  list = serv.get_compounds_by_pathway("path:map00010")
-  list.each do |compound|
-    puts compound
-  end
-
-  puts "### get_compounds_by_pathway('path:eco00010')"
-  list = serv.get_compounds_by_pathway("path:eco00010")
-  list.each do |compound|
-    puts compound
-  end
-
-  puts "### get_reactions_by_pathway('path:map00010')"
-  list = serv.get_reactions_by_pathway("path:map00010")
-  list.each do |reaction|
-    puts reaction
-  end
-
-  puts "### get_reactions_by_pathway('path:eco00010')"
-  list = serv.get_reactions_by_pathway("path:eco00010")
-  list.each do |reaction|
-    puts reaction
-  end
-
-  puts "==== pathway by objects"
-
-  puts "### get_pathways_by_genes(['eco:b0756', 'eco:b1002'])"
-  list = serv.get_pathways_by_genes(["eco:b0756", "eco:b1002"])
-  list.each do |path|
-    puts path
-  end
-
-  puts "### get_pathways_by_enzymes(['ec:5.1.3.3', 'ec:3.1.3.10'])"
-  list = serv.get_pathways_by_enzymes(["ec:5.1.3.3", "ec:3.1.3.10"])
-  list.each do |path|
-    puts path
-  end
-
-  puts "### get_pathways_by_compounds(['cpd:C00221', 'cpd:C00267'])"
-  list = serv.get_pathways_by_compounds(["cpd:C00221", "cpd:C00267"])
-  list.each do |path|
-    puts path
-  end
-
-  puts "### get_pathways_by_reactions(['rn:R00014', 'rn:R00710'])"
-  list = serv.get_pathways_by_reactions(["rn:R00014", "rn:R00710"])
-  list.each do |path|
-    puts path
-  end
-
-  puts "==== relation between objects"
-
-  puts "### get_linked_pathways('path:eco00620')"
-  list = serv.get_linked_pathways('path:eco00620')
-  list.each do |path|
-    puts path
-  end
-
-  puts "### get_genes_by_enzyme('ec:1.1.1.1', 'eco')"
-  list = serv.get_genes_by_enzyme("ec:1.1.1.1", "eco")
-  list.each do |gene|
-    puts gene
-  end
-
-  puts "### get_enzymes_by_gene('eco:b0002')"
-  list = serv.get_enzymes_by_gene("eco:b0002")
-  list.each do |enzyme|
-    puts enzyme
-  end
-
-  puts "### get_enzymes_by_compound('cpd:C00345')"
-  list = serv.get_enzymes_by_compound("cpd:C00345")
-  list.each do |enzyme|
-    puts enzyme
-  end
-
-  puts "### get_enzymes_by_reaction('rn:R00100')"
-  list = serv.get_enzymes_by_reaction("rn:R00100")
-  list.each do |enzyme|
-    puts enzyme
-  end
-
-  puts "### get_compounds_by_enzyme('ec:2.7.1.12')"
-  list = serv.get_compounds_by_enzyme("ec:2.7.1.12")
-  list.each do |compound|
-    puts compound
-  end
-
-  puts "### get_compounds_by_reaction('rn:R00100')"
-  list = serv.get_compounds_by_reaction("rn:R00100")
-  list.each do |compound|
-    puts compound
-  end
-  
-  puts "### get_reactions_by_enzyme('ec:2.7.1.12')"
-  list = serv.get_reactions_by_enzyme("ec:2.7.1.12")
-  list.each do |reaction|
-    puts reaction
-  end
-
-  puts "### get_reactions_by_compound('cpd:C00199')"
-  list = serv.get_reactions_by_compound("cpd:C00199")
-  list.each do |reaction|
-    puts reaction
-  end
-  
-  puts "=== GENES"
-
-  puts "### get_genes_by_organism('mge', 1, 5)"
-  list = serv.get_genes_by_organism("mge", 1, 5)
-  list.each do |gene|
-    puts gene
-  end
-
-  puts "# * get_all_genes_by_organism('mge')"
-  list = serv.get_all_genes_by_organism("mge")
-  list.each do |gene|
-    puts gene
-  end
-  
-  puts "=== GENOME"
-
-  puts "### get_number_of_genes_by_organism(org)"
-  puts serv.get_number_of_genes_by_organism("mge")
-
-end
-