bio 1.5.2 → 1.6.0.pre.20181210

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

@@ -1,101 +0,0 @@
-#
-# = 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/midi.rb

@@ -1,430 +0,0 @@
-#
-# = 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
-