wwood-bioruby 1.2.11

data/lib/bio/shell/plugin/flatfile.rb

@@ -0,0 +1,101 @@
+#
+# = bio/shell/plugin/flatfile.rb - plugin for flatfile database
+#
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: flatfile.rb,v 1.13 2007/04/05 23:45:11 trevor Exp $
+#
+
+module Bio::Shell
+
+  private
+
+  def flatfile(filename)
+    if block_given?
+      Bio::FlatFile.auto(filename) do |flat|
+        flat.each do |entry|
+          yield flat.entry_raw
+        end
+      end
+    else
+      entry = ''
+      Bio::FlatFile.auto(filename) do |flat|
+        flat.next_entry
+        entry = flat.entry_raw
+      end
+      return entry
+    end
+  end
+
+  def flatauto(filename)
+    if block_given?
+      Bio::FlatFile.auto(filename) do |flat|
+        flat.each do |entry|
+          yield entry
+        end
+      end
+    else
+      entry = ''
+      Bio::FlatFile.auto(filename) do |flat|
+        entry = flat.next_entry
+      end
+      return entry
+    end
+  end
+
+  def flatparse(entry)
+    if cls = Bio::FlatFile.autodetect(entry)
+      return cls.new(entry)
+    end
+  end
+
+  def flatfasta(fastafile, *flatfiles)
+    puts "Saving fasta file (#{fastafile}) ... "
+    File.open(fastafile, "w") do |fasta|
+      flatfiles.each do |flatfile|
+        puts "  converting -- #{flatfile}"
+        Bio::FlatFile.auto(flatfile) do |flat|
+          flat.each do |entry|
+            header = "#{entry.entry_id} #{entry.definition}"
+            fasta.puts entry.seq.to_fasta(header, 50)
+          end
+        end
+      end
+    end
+    puts "done"
+  end
+
+  def flatindex(dbname, *flatfiles)
+    begin
+      dir = Bio::Shell.create_flat_dir(dbname)
+      print "Creating BioFlat index (#{dir}) ... "
+      bdb = format = options = nil
+      Bio::FlatFileIndex.makeindex(bdb, dir, format, options, *flatfiles)
+      puts "done"
+    rescue
+      warn "Error: Failed to create index (#{dir}) : #{$!}"
+    end
+  end
+
+  def flatsearch(dbname, keyword)
+    dir = Bio::Shell.find_flat_dir(dbname)
+    unless dir
+      warn "Error: Failed to open database (#{dbname})"
+      return
+    end
+    entry = ''
+    Bio::FlatFileIndex.open(dir) do |db|
+      if results = db.include?(keyword)
+        results.each do |entry_id|
+          entry << db.search_primary(entry_id).to_s
+        end
+      else
+        warn "Error: No hits found in #{dbname} (#{keyword})"
+      end
+    end
+    return entry
+  end
+
+end

data/lib/bio/shell/plugin/keggapi.rb

@@ -0,0 +1,181 @@
+#
+# = bio/shell/plugin/keggapi.rb - plugin for KEGG API
+#
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: keggapi.rb,v 1.12 2007/04/05 23:35:41 trevor Exp $
+#
+
+module Bio::Shell
+
+  module Private
+
+    module_function
+
+    def keggapi_definition2tab(list)
+      ary = []
+      list.each do |entry|
+        ary << "#{entry.entry_id}\t#{entry.definition}"
+      end
+      return ary
+    end
+  end
+
+  private
+
+  def keggapi(wsdl = nil)
+    if wsdl
+      @keggapi = Bio::KEGG::API.new(wsdl)
+    else
+      @keggapi ||= Bio::KEGG::API.new
+    end
+    return @keggapi
+  end
+
+  # DBGET
+
+  def binfo(db = "all")
+    result = keggapi.binfo(db)
+    puts result
+    return result
+  end
+
+  def bfind(str)
+    result = keggapi.bfind(str)
+    return result
+  end
+
+  def bget(str)
+    result = keggapi.bget(str)
+    if block_given?
+      yield result
+    else
+      puts result
+      return result
+    end
+  end
+
+  def btit(str)
+    result = keggapi.btit(str)
+    puts result
+    return result
+  end
+
+  def bconv(str)
+    result = keggapi.bconv(str)
+    puts result
+    return result
+  end
+
+  # DATABASES
+
+  def keggdbs
+    list = keggapi.list_databases
+    result = Bio::Shell::Private.keggapi_definition2tab(list).join("\n")
+    puts result
+    return list.map {|x| x.entry_id}
+  end
+
+  def keggorgs
+    list = keggapi.list_organisms
+    result = Bio::Shell::Private.keggapi_definition2tab(list).sort.join("\n")
+    puts result
+    return list.map {|x| x.entry_id}
+  end
+
+  def keggpathways(org = "map")
+    list = keggapi.list_pathways(org)
+    result = Bio::Shell::Private.keggapi_definition2tab(list).join("\n")
+    puts result
+    return list.map {|x| x.entry_id}
+  end
+
+  # use KEGG DAS insetad
+  def kegggenomeseq(org)
+    result = ""
+    require 'net/ftp'
+    Net::FTP.open("ftp.genome.jp", "anonymous") do |ftp|
+      path = "/pub/kegg/genomes/#{org}"
+      list = ftp.nlst(path)
+      file = list.grep(/.*genome$/).shift
+      if file
+        open("ftp://ftp.genome.jp/#{file}") do |file|
+          result = file.read
+        end
+      end
+    end
+    return result
+  end
+
+end
+
+=begin
+
+== BioRuby extensions
+
+--- get_all_best_best_neighbors_by_gene(genes_id)
+--- get_all_best_neighbors_by_gene(genes_id)
+--- get_all_reverse_best_neighbors_by_gene(genes_id)
+--- get_all_paralogs_by_gene(genes_id)
+--- get_all_genes_by_motifs(motif_id_list)
+--- get_all_oc_members_by_gene(genes_id)
+--- get_all_pc_members_by_gene(genes_id)
+--- get_all_genes_by_organism(org)
+--- get_all_linkdb_by_entry(entry_id, db)
+--- save_image(url, filename = nil)
+--- get_entries(ary = [])
+--- get_aaseqs(ary = [])
+--- get_naseqs(ary = [])
+--- get_definitions(ary = [])
+
+== Original KEGG API methods
+
+--- get_linkdb_by_entry(entry_id, db, start, max_results)
+--- get_best_best_neighbors_by_gene(genes_id, start, max_results)
+--- get_best_neighbors_by_gene(genes_id, start, max_results)
+--- get_reverse_best_neighbors_by_gene(genes_id, start, max_results)
+--- get_paralogs_by_gene(genes_id, start, max_results)
+--- get_motifs_by_gene(genes_id, db)
+--- get_genes_by_motifs(motif_id_list, start, max_results)
+--- get_ko_by_gene(genes_id)
+--- get_ko_by_ko_class(ko_class_id)
+--- get_genes_by_ko_class(ko_class_id, org, start, max_results)
+--- get_genes_by_ko(ko_id, org)
+--- get_oc_members_by_gene(genes_id, start, max_results)
+--- get_pc_members_by_gene(genes_id, start, max_results)
+--- mark_pathway_by_objects(pathway_id, object_id_list)
+--- color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
+--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
+--- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
+--- get_genes_by_pathway(pathway_id)
+--- get_enzymes_by_pathway(pathway_id)
+--- get_compounds_by_pathway(pathway_id)
+--- get_glycans_by_pathway(pathway_id)
+--- get_reactions_by_pathway(pathway_id)
+--- get_kos_by_pathway(pathway_id)
+--- get_pathways_by_genes(genes_id_list)
+--- get_pathways_by_enzymes(enzyme_id_list)
+--- get_pathways_by_compounds(compound_id_list)
+--- get_pathways_by_glycans(glycan_id_list)
+--- get_pathways_by_reactions(reaction_id_list)
+--- get_pathways_by_kos(ko_id_list, org)
+--- get_linked_pathways(pathway_id)
+--- get_genes_by_enzyme(enzyme_id, org)
+--- get_enzymes_by_gene(genes_id)
+--- get_enzymes_by_compound(compound_id)
+--- get_enzymes_by_glycan(glycan_id)
+--- get_enzymes_by_reaction(reaction_id)
+--- get_compounds_by_enzyme(enzyme_id)
+--- get_compounds_by_reaction(reaction_id)
+--- get_glycans_by_enzyme(enzyme_id)
+--- get_glycans_by_reaction(reaction_id)
+--- get_reactions_by_enzyme(enzyme_id)
+--- get_reactions_by_compound(compound_id)
+--- get_reactions_by_glycan(glycan_id)
+--- get_genes_by_organism(org, start, max_results)
+--- get_number_of_genes_by_organism(org)
+--- convert_mol_to_kcf(mol_text)
+
+=end

data/lib/bio/shell/plugin/midi.rb

@@ -0,0 +1,430 @@
+#
+# = bio/shell/plugin/midi.rb - Sequence to MIDI converter
+#
+# Copyright::   Copyright (C) 2003, 2005
+#               Natsuhiro Ichinose <ichinose@genome.ist.i.kyoto-u.ac.jp>,
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: midi.rb,v 1.9 2007/04/05 23:35:41 trevor Exp $
+#
+
+#--
+# *TODO*
+#   - add "Ohno" style
+#   - add a accessor to drum pattern
+#   - add a new feature to select music style (pop, trans, ryukyu, ...)
+#   - what is the base?
+#++
+
+class Bio::Sequence::NA
+
+  class MidiTrack
+
+    MidiProg = [
+      "Acoustic Grand Piano",
+      "Bright Acoustic Piano",
+      "Electric grand Piano",
+      "Honky Tonk Piano",
+      "Eiectric Piano 1",
+      "Electric Piano 2",
+      "Harpsichord",
+      "Clavinet",
+      "Celesra",
+      "Glockenspiel",
+      "Music Box",
+      "Vibraphone",
+      "Marimba",
+      "Xylophone",
+      "Tubular bells",
+      "Dulcimer",
+      "Drawbar Organ",
+      "Percussive Organ",
+      "Rock Organ",
+      "Church Organ",
+      "Reed Organ",
+      "Accordion",
+      "Harmonica",
+      "Tango Accordion",
+      "Nylon Accustic Guitar",
+      "Steel Acoustic Guitar",
+      "Jazz Electric Guitar",
+      "Ciean Electric Guitar",
+      "Muted Electric Guitar",
+      "Overdrive Guitar",
+      "Distorted Guitar",
+      "Guitar Harmonics",
+      "Acoustic Bass",
+      "Electric Fingered Bass",
+      "Electric Picked Bass",
+      "Fretless Bass",
+      "Slap Bass 1",
+      "Slap Bass 2",
+      "Syn Bass 1",
+      "Syn Bass 2",
+      "Violin",
+      "Viola",
+      "Cello",
+      "Contrabass",
+      "Tremolo Strings",
+      "Pizzicato Strings",
+      "Orchestral Harp",
+      "Timpani",
+      "String Ensemble 1",
+      "String Ensemble 2 (Slow)",
+      "Syn Strings 1",
+      "Syn Strings 2",
+      "Choir Aahs",
+      "Voice Oohs",
+      "Syn Choir",
+      "Orchestral Hit",
+      "Trumpet",
+      "Trombone",
+      "Tuba",
+      "Muted Trumpet",
+      "French Horn",
+      "Brass Section",
+      "Syn Brass 1",
+      "Syn Brass 2",
+      "Soprano Sax",
+      "Alto Sax",
+      "Tenor Sax",
+      "Baritone Sax",
+      "Oboe",
+      "English Horn",
+      "Bassoon",
+      "Clarinet",
+      "Piccolo",
+      "Flute",
+      "Recorder",
+      "Pan Flute",
+      "Bottle Blow",
+      "Shakuhachi",
+      "Whistle",
+      "Ocarina",
+      "Syn Square Wave",
+      "Syn Sawtooth Wave",
+      "Syn Calliope",
+      "Syn Chiff",
+      "Syn Charang",
+      "Syn Voice",
+      "Syn Fifths Sawtooth Wave",
+      "Syn Brass & Lead",
+      "New Age Syn Pad",
+      "Warm Syn Pad",
+      "Polysynth Syn Pad",
+      "Choir Syn Pad",
+      "Bowed Syn Pad",
+      "Metal Syn Pad",
+      "Halo Syn Pad",
+      "Sweep Syn Pad",
+      "SFX Rain",
+      "SFX Soundtrack",
+      "SFX Crystal",
+      "SFX Atmosphere",
+      "SFX Brightness",
+      "SFX Goblins",
+      "SFX Echoes",
+      "SFX Sci-fi",
+      "Sitar",
+      "Banjo",
+      "Shamisen",
+      "Koto",
+      "Kalimba",
+      "Bag Pipe",
+      "Fiddle",
+      "Shanai",
+      "Tinkle Bell",
+      "Agogo",
+      "Steel Drums",
+      "Woodblock",
+      "Taiko Drum",
+      "Melodic Tom",
+      "Syn Drum",
+      "Reverse Cymbal",
+      "Guitar Fret Noise",
+      "Breath Noise",
+      "Seashore",
+      "Bird Tweet",
+      "Telephone Ring",
+      "Helicopter",
+      "Applause",
+      "Gun Shot"
+    ]
+
+    Styles = {
+  #    "Ohno" => {
+  #      # http://home.hiroshima-u.ac.jp/cato/bunkakoryuron.html
+  #    },
+      "Ichinose" => {
+        :tempo => 120,
+        :scale => [0, 2, 4, 5, 7, 9, 11],
+        :tones => [
+          {:prog =>  9, :base => 60, :range => 2},
+          {:prog => 13, :base => 48, :range => 2},
+          {:prog => 41, :base => 48, :range => 2},
+          {:prog => 44, :base => 36, :range => 2},
+        ]
+      },
+      "Okinawan" => {
+        :tempo => 180,
+        :scale => [0,4,5,7,11],
+        :tones => [
+          {:prog => MidiProg.index("Harpsichord"),   :base => 60, :range => 2},
+          {:prog => MidiProg.index("Dulcimer"),      :base => 48, :range => 2},
+          {:prog => MidiProg.index("Fretless Base"), :base => 36, :range => 1},
+        ]
+      },
+      "Major" => {
+        :scale => [0,2,4,5,7,9,11],
+      },
+      "Minor" => {
+        :scale => [0,2,3,5,7,9,10],
+      },
+      "Harmonic minor" => {
+        :scale => [0,2,3,5,7,9,11],
+      },
+      "Whole tone" => {
+        :scale => [0,2,4,6,8,10],
+      },
+      "Half tone" => {
+        :scale => [0,1,2,3,4,5,6,7,8,9,10,11],
+      },
+      "Indian" => {
+        :scale => [0,1,4,5,7,8,11],
+      },
+      "Arabic" => {
+        :scale => [0,2,3,6,7,8,11],
+      },
+      "Spanish" => {
+        :scale => [0,1,3,4,5,7,8,10],
+      },
+      "Japanese" => {
+        :scale => [0,2,5,7,9],
+      },
+    }
+
+    def initialize(channel = 0, program = nil, base = nil, range = nil, scale = nil)
+      @channel = channel & 0xff
+      @program = program || 0
+      @base    = base    || 60
+      @range   = range   || 2
+      @scale   = scale   || [0, 2, 4, 5, 7, 9, 11]
+
+      @tunes   = []
+      @tune    = 0
+      @code    = []
+      @time    = 0
+
+      @range.times do |i|
+        @scale.each do |c|
+          @tunes.push c + i * 12
+        end
+      end
+
+      @ttype = {
+        'aa' =>  1, 'at' =>  0, 'ac' => 3, 'ag' => -1,
+        'ta' =>  0, 'tt' => -1, 'tc' => 1, 'tg' => -2,
+        'ca' =>  2, 'ct' =>  1, 'cc' => 2, 'cg' =>  6,
+        'ga' => -1, 'gt' => -3, 'gc' => 0, 'gg' => -2,
+      }
+      @dtype = [
+        { 'aa' => 2, 'at' => 4, 'ac' => 4, 'ag' => 2,
+          'ta' => 2, 'tt' => 4, 'tc' => 4, 'tg' => 2,
+          'ca' => 2, 'ct' => 3, 'cc' => 1, 'cg' => 2,
+          'ga' => 1, 'gt' => 2, 'gc' => 2, 'gg' => 3,
+        },
+        { 'aa' => 3, 'at' => 3, 'ac' => 2, 'ag' => 3,
+          'ta' => 3, 'tt' => 3, 'tc' => 2, 'tg' => 2,
+          'ca' => 3, 'ct' => 2, 'cc' => 1, 'cg' => 1,
+          'ga' => 1, 'gt' => 1, 'gc' => 1, 'gg' => 1,
+        },
+        { 'aa' => 2, 'at' => 2, 'ac' => 2, 'ag' => 2,
+          'ta' => 1, 'tt' => 1, 'tc' => 2, 'tg' => 2,
+          'ca' => 2, 'ct' => 2, 'cc' => 2, 'cg' => 3,
+          'ga' => 2, 'gt' => 2, 'gc' => 3, 'gg' => 1,
+        },
+        { 'aa' => 1, 'at' => 1, 'ac' => 1, 'ag' => 1,
+          'ta' => 1, 'tt' => 1, 'tc' => 1, 'tg' => 1,
+          'ca' => 1, 'ct' => 1, 'cc' => 1, 'cg' => 3,
+          'ga' => 1, 'gt' => 1, 'gc' => 1, 'gg' => 1,
+        },
+      ]
+
+      @code.concat [0x00, 0xc0 | (@channel & 0xff)]
+      @code.concat icode(@program & 0xff, 1)
+    end
+
+    def icode(num, n)
+      code = []
+      n.times do |i|
+        code.push num & 0xff
+        num >>= 8
+      end
+      code.reverse
+    end
+
+    def rcode(num)
+      code = []
+      code.push num & 0x7f
+      while num > 0x7f
+        num >>= 7
+        code.push num & 0x7f | 0x80
+      end
+      code.reverse
+    end
+
+    def c2s(code)
+      ans = ""
+      code.each do |c|
+        ans += c.chr
+      end
+      ans
+    end
+
+    def push(s)
+      tt = @time % 4
+      t = @ttype[s[0, 2]]
+      d = @dtype[tt][s[2, 2]]
+      if !t.nil? && !d.nil?
+        @tune += t
+        @tune %= @tunes.length
+        if tt == 0
+          vel = 90
+        elsif tt == 1 && d > 1
+          vel = 100
+        elsif tt == 2
+          vel = 60
+        else
+          vel = 50
+        end
+        @code.concat rcode(1)
+        @code.concat [0x90 | @channel, @tunes[@tune] + @base, vel]
+        @code.concat rcode(240 * d)
+        @code.concat [0x80 | @channel, @tunes[@tune] + @base, 0]
+        @time += d
+      end
+    end
+
+    def push_silent(d)
+      @code.concat rcode(1)
+      @code.concat [0x90 | @channel, 0, 0]
+      @code.concat rcode(240 * d)
+      @code.concat [0x80 | @channel, 0, 0]
+      @time += d;
+    end
+
+    def encode
+      ans ="MTrk"
+      ans += c2s(icode(@code.length + 4, 4))
+      ans += c2s(@code)
+      ans += c2s([0x00, 0xff, 0x2f, 0x00])
+      ans
+    end
+
+    def header(num, tempo = 120)
+      ans = "MThd"
+      ans += c2s(icode(6, 4))
+      ans += c2s(icode(1, 2))
+      ans += c2s(icode(num + 1, 2))
+      ans += c2s(icode(480, 2))
+      ans += "MTrk"
+      ans += c2s(icode(11, 4))
+      ans += c2s([0x00, 0xff, 0x51, 0x03])
+      ans += c2s(icode(60000000 / tempo, 3))
+      ans += c2s([0x00, 0xff, 0x2f, 0x00])
+      ans
+    end
+
+  end # MidiTrack
+
+
+  # style:
+  #   Hash of :tempo, :scale, :tones
+  # scale:
+  #   C  C# D  D# E  F  F# G  G# A  A#  B
+  #   0  1  2  3  4  5  6  7  8  9  10  11
+  # tones:
+  #   Hash of :prog, :base, :range -- tone, vol? or len?, octaves
+  # drum:
+  #   true (with rhythm part), false (without rhythm part)
+  def to_midi(style = {}, drum = true)
+    default = MidiTrack::Styles["Ichinose"]
+    if style.is_a?(String)
+      style = MidiTrack::Styles[style] || default
+    end
+    tempo = style[:tempo] || default[:tempo]
+    scale = style[:scale] || default[:scale]
+    tones = style[:tones] || default[:tones]
+
+    track = []
+
+    tones.each_with_index do |tone, i|
+      ch = i
+      ch += 1 if i >= 9         # skip rythm track
+      track.push MidiTrack.new(ch, tone[:prog], tone[:base], tone[:range], scale)
+    end
+
+    if drum
+      rhythm = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]
+      track.push(MidiTrack.new(9, 0, 35, 2, rhythm))
+    end
+
+    cur = 0
+    window_search(4) do |s|
+      track[cur % track.length].push(s)
+      cur += 1
+    end
+
+    track.each do |t|
+      t.push_silent(12)
+    end
+
+    ans = track[0].header(track.length, tempo)
+    track.each do |t|
+      ans += t.encode
+    end
+    return ans
+  end
+
+end
+
+
+module Bio::Shell
+
+  private
+
+  def midifile(filename, seq, *args)
+    begin
+      print "Saving MIDI file (#{filename}) ... "
+      File.open(filename, "w") do |file|
+        file.puts seq.to_midi(*args)
+      end
+      puts "done"
+    rescue
+      warn "Error: Failed to save (#{filename}) : #{$!}"
+    end
+  end
+
+end
+
+
+if $0 == __FILE__
+
+  # % for i in file*
+  # do
+  #   ruby -r bio bio/shell/plugin/midi.rb $i ${i}.mid
+  # done
+
+  include Bio::Shell
+
+  seq_file = ARGV.shift
+  mid_file = ARGV.shift
+
+  Bio::FlatFile.auto(seq_file) do |ff|
+    ff.each do |f|
+      midifile(mid_file, f.naseq[0..1000])
+    end
+  end
+end
+