sequence_logo 1.1.2 → 1.2.0

data/lib/sequence_logo/ytilib/pmsd.rb

@@ -1,99 +0,0 @@
-#!/usr/bin/ruby
-module Ytilib
-  class PM
-    def score_sigma(trycount = 4**10, approx = false, bg = nil)
-      
-      scores = []
-      if @size <= 10 && !approx
-        (0...4**@size).each { |i| 
-          word = i.to_s(4).rjust(@size, "0").tr("0123", "ACGT")
-          scores << score(word)
-        }
-      else
-        trycount.times {
-          word = bg ? Randoom.rand_seq(@size, bg) : Randoom.rand_seq(@size)
-          scores << score(word)
-        }
-      end
-      sum1 = scores.inject(0) { |sum,s| sum += s }
-      mean = sum1 / scores.size
-      
-      sum2, sumc = 0, 0
-      scores.each { |score|
-        sum2 += (score-mean)**2
-        sumc += (score-mean)
-      }
-      variance = (sum2 - sumc**2 / scores.size) / (scores.size-1)
-      
-      sigma = Math.sqrt(variance)
-      if block_given?
-        yield(sigma, mean)
-      end
-      
-      return sigma
-    end
-    
-    def fast_score_sigma
-      n, mean, m2 = 0, 0, 0
-      
-      recursive_walk([matrix['A'],matrix['C'],matrix['G'],matrix['T']], 0, 0) { |x|
-        n = n + 1
-        delta = x - mean
-        mean = mean + delta/n
-        m2 = m2 + delta*(x-mean)
-      }
-      
-      variance = m2/(n - 1)
-      
-      if block_given?
-        yield(sigma = Math.sqrt(variance), mean)
-      end
-      
-      return sigma
-    end
-    
-    def fast_score_sigma_precise
-      n, mean = 0, 0
-      
-      recursive_walk([matrix['A'],matrix['C'],matrix['G'],matrix['T']], 0, 0) { |x|
-        n += 1
-        delta = x - mean
-        mean = mean + delta/n
-      }
-      
-      n, m2 = 0, 0
-      recursive_walk([matrix['A'],matrix['C'],matrix['G'],matrix['T']], 0, 0) { |x|
-        n = n + 1
-        delta = x - mean
-        m2 = m2 + delta*(x-mean)
-      }
-      
-      variance = m2/(n - 1)
-      
-      if block_given?
-        yield(sigma = Math.sqrt(variance), mean)
-      end
-      
-      return sigma
-    end
-    
-  private
-    def recursive_walk(matrix, score, i)
-      if i < @size
-        
-        recursive_walk(matrix, score + matrix[0][i], i+1) { |x| yield x }
-        recursive_walk(matrix, score + matrix[1][i], i+1) { |x| yield x }
-        recursive_walk(matrix, score + matrix[2][i], i+1) { |x| yield x }
-        recursive_walk(matrix, score + matrix[3][i], i+1) { |x| yield x }
-        
-      else
-        if block_given?
-          yield(score)
-        else
-          raise "no block for recursive walk"
-        end
-      end
-    end
-  
-  end
-end

data/lib/sequence_logo/ytilib/randoom.rb

@@ -1,131 +0,0 @@
-#!/usr/bin/ruby
-module Ytilib
-
-srand
-
-module Randoom
-  
-  private
-
-  def Randoom.new_counts
-    { 'A' => 0, 'C' => 0, 'G' => 0, 'T' => 0, 'N' => 0 }
-  end
-  
-  def Randoom.random_letter(probs)
-    random = rand()
-    return 'A' if random < probs['A']
-    return 'C' if random < probs['A'] + probs['C']
-    return 'G' if random < probs['A'] + probs['C'] + probs['G']
-    return 'T'
-  end
-
-  public
-  
-  def Randoom.calc_probs(input)
-    counts = new_counts
-    counts.default = 0
-    (0...input.length).each { |i|
-      counts[input[i,1].upcase] += 1
-    }
-    return make_probs!(counts)
-  end
-    
-  def Randoom.rand_seq(req_len, probs = DEF_PROBS, probs_m = nil)
-    randoom = ''
-    if (probs_m == nil)
-      req_len.times { randoom << random_letter(probs) }
-      return randoom  
-    end
-    random_l = random_letter(probs)
-    randoom = random_l
-    (req_len-1).times {
-      cur_probs = probs_m[random_l]
-      random_l = random_letter(cur_probs)
-      randoom << random_l
-    }
-    return randoom
-  end
-  
-  def Randoom.calc_probs_m(input)
-    probs_m = { 'A' => {}, 'C' => {}, 'G' => {}, 'T' => {} }
-    counts = { 'A' => new_counts, 'C' => new_counts, 'G' => new_counts, 'T' => new_counts, 'N' => new_counts }
-    (0...input.length-1).each { |i|
-      pair = input[i, 2].upcase
-      counts[pair[0,1]][pair[1,1]] += 1
-    }
-    probs_m['A'] = make_probs!(counts['A'])
-    probs_m['C'] = make_probs!(counts['C'])
-    probs_m['G'] = make_probs!(counts['G'])
-    probs_m['T'] = make_probs!(counts['T'])
-    return probs_m
-  end
-  
-  def Randoom.make_probs_m!(counts)
-    ['A','C','G','T','N'].each { |l2|
-      addv = counts['N'][l2] / 4.0
-      ['A','C','G','T'].each { |l1|
-        counts[l1][l2] += addv
-      }
-    }
-    
-    probs_m = { 'A' => {}, 'C' => {}, 'G' => {}, 'T' => {} }
-    probs_m['A'] = make_probs!(counts['A'])
-    probs_m['C'] = make_probs!(counts['C'])
-    probs_m['G'] = make_probs!(counts['G'])
-    probs_m['T'] = make_probs!(counts['T'])
-    return probs_m
-  end
-  
-  def Randoom.make_probs!(counts, length = nil)
-    probs = { 'A' => 0, 'C' => 0, 'G' => 0, 'T' => 0 }
-    length = counts['A'] + counts['C'] + counts['G'] + counts['T'] + counts['N'] if length == nil
-    length = length.to_f
-    ['A','C','G','T'].each { |l| counts[l] += counts['N'] / 4.0 }
-    return probs if length == 0
-    probs['A'] = counts['A'] / length
-    probs['C'] = counts['C'] / length
-    probs['G'] = counts['G'] / length
-    probs['T'] = 1 - probs['A'] - probs['C'] - probs['G']
-    return probs
-  end
-  
-  def Randoom.equalize!(probs)
-    probs['A'] = probs['T'] = (probs['A'] + probs['T']) / 2
-    probs['C'] = probs['G'] = (probs['C'] + probs['G']) / 2
-    return probs
-  end
-  
-  def Randoom.twostrand!(probs)
-    return Randoom.equalize!(probs)
-  end
-  
-  DEF_PROBS = PPM.probs2IUPAC!({ 'A' => 0.25, 'C' => 0.25, 'G' => 0.25, 'T' => 0.25, 'N' => 0.25 })
-  
-  # probabilities counted without _random.fa files for human genome
-  DMEL40_PROBS1 = {"A"=>0.287729562173578, "C"=>0.21236364146414, "G"=>0.212259972960341, "T"=>0.287646823401942}
-  DMEL40_PROBS2 = {"A"=>0.28768819278776, "C"=>0.21231180721224, "G"=>0.21231180721224, "T"=>0.28768819278776}
-  
-  DMEL40_PROBS1_M = {"A"=>{"A"=>0.350403075314602, "C"=>0.181194374386404, "G"=>0.188361404205017, "T"=>0.280041146093977}, 
-    "C"=>{"A"=>0.325366772443085, "C"=>0.222264645612127, "G"=>0.197213801868993, "T"=>0.255154780075794}, 
-    "G"=>{"A"=>0.260710563672393, "C"=>0.27150575901391, "G"=>0.222294234776053, "T"=>0.245489442537644}, 
-    "T"=>{"A"=>0.217189093089999, "C"=>0.192590127484359, "G"=>0.239869076706963, "T"=>0.350351702718679}}
-  
-  HG17_PROBS1 = {"A"=>0.295309361730334, "C"=>0.204413561169847, "G"=>0.204519414193999, "T"=>0.295757662905821}
-  HG17_PROBS2 = {"A"=>0.295533512318077, "C"=>0.204466487681923, "G"=>0.204466487681923, "T"=>0.295533512318077}
-  
-  HG17_PROBS1_M = {"A"=>{"A"=>0.331091206257755, "C"=>0.170458424092748, "G"=>0.236770972081246, "T"=>0.261679397568252}, 
-    "C"=>{"A"=>0.354813019140533, "C"=>0.254741288394943, "G"=>0.0481667110625576, "T"=>0.342278981401966}, 
-    "G"=>{"A"=>0.290057117684408, "C"=>0.208514091370804, "G"=>0.254732297362797, "T"=>0.246696493581991}, 
-    "T"=>{"A"=>0.222087715262152, "C"=>0.200697606508443, "G"=>0.245657322003887, "T"=>0.331557356225517}}
-  
-  HG18_PROBS1 = {"A"=>0.291900580635872, "C"=>0.207855064518284, "G"=>0.207968587245859, "T"=>0.292275767599985}
-  HG18_PROBS2 = {"A"=>0.292088174117929, "C"=>0.207911825882071, "G"=>0.207911825882071, "T"=>0.292088174117929}
-  
-  MM9_PROBS1 = {"A"=>0.289755259854654, "C"=>0.210085673636132, "G"=>0.210143929198141, "T"=>0.290015137311074}
-  MM9_PROBS2 = {"A"=>0.289885198582864, "C"=>0.210114801417136, "G"=>0.210114801417136, "T"=>0.289885198582864}
-  
-  MM9_PROBS1_M = {"A"=>{"A"=>0.310389104265713, "C"=>0.184962574392377, "G"=>0.251904718465914, "T"=>0.252743602875996}, "C"=>{"A"=>0.352189584318682, "C"=>0.250794045222924, "G"=>0.0494404816637487, "T"=>0.347575888794645}, "G"=>{"A"=>0.295931117515178, "C"=>0.197870954111653, "G"=>0.250756985626016, "T"=>0.255440942747154}, "T"=>{"A"=>0.219437756702452, "C"=>0.214548041970626, "G"=>0.255405334730743, "T"=>0.310608866596179}}
-
-end
-
-end

data/lib/sequence_logo/ytilib/ytilib.rb

@@ -1,147 +0,0 @@
-module Ytilib
-  def Ytilib.time
-    return Time.now.strftime('%d %b %H:%M:%S')
-  end
-end
-
-$program_name = nil
-
-def start(fullpath)
-  report(fullpath + ARGV.inject("") { |out, v| out += " " + v})
-  return if $NO_REPORT
-  $program_name = "[#{File.name_wo_ext(fullpath)}]"
-end
-
-def report(message, program_name = nil)
-  $program_name = "[#{program_name}]" if program_name != nil
-  return if $NO_REPORT
-  puts "LLIB #{Ytilib.time} #{$program_name}\t#{message}" if !block_given? || yield
-end
-
-def checkerr(message = "checkerr failed")  
-  if !block_given? || yield
-    puts "LLIB #{Ytilib.time} [error]\t#{message}" unless $NO_REPORT
-    raise "LLIB #{Ytilib.time} #{$program_name}\n\t#{message}\n" 
-  end
-end
-
-module Ytilib
-  
-  STRAND_DIRECT = "direct"
-  STRAND_REVCOMP = "revcomp"  
-  
-  def Ytilib.read_mfa2hash(path)
-    input_fasta_f = File.new(path, "r")
-    seqs, seq_name = {}, nil
-    input_fasta_f.each_line { |line|
-      if line[0,1] == ">"
-        seq_name = line[1..-1].strip
-        seq_name = yield seq_name if block_given?
-        checkerr("multiple sequences with the same name=#{seq_name}") { seqs[seq_name] }
-        seqs[seq_name] = ""
-      elsif seq_name != nil
-        seqs[seq_name] << line.strip
-      end
-    }
-    input_fasta_f.close
-    return seqs
-  end
-  
-  def Ytilib.read_mfa2array(path)
-    input_fasta_f = File.new(path, "r")
-    seqs, seq_name = [], nil
-    input_fasta_f.each_line { |line|
-      if line[0,1] == ">"
-        seq_name = line[1..-1].strip
-        yield seq_name if block_given?
-        seqs << ""
-      elsif seq_name != nil
-        seqs.last << line.strip
-      end
-    }
-    input_fasta_f.close
-    return seqs
-  end
-  
-  def Ytilib.mfa2array(input)
-    seqs, seq_name = [], nil
-    input.each_line { |line|
-      if line[0,1] == ">"
-        seq_name = line[1..-1].strip
-        seqs << ""
-      elsif seq_name != nil
-        seqs.last << line.strip
-      end
-    }
-    return seqs
-  end
-  
-  def Ytilib.read_plain2array(path)
-    array = []
-    File.open(path).each_line { |line|
-      array << line.strip if !line.strip.empty?
-    }
-    return array
-  end  
-  
-  def Ytilib.read_seqs2array(path)
-    type = File.ext_wo_name(path)
-    case type
-    when "mfa", "fasta", "fa"
-      return Ytilib.read_mfa2array(path)
-    when "plain","txt"
-      return Ytilib.read_plain2array(path)
-    else
-      checkerr("unknown sequences-file, ext=#{type}")
-    end
-  end
-  
-  def Ytilib.write_mfa(seqs, path, prefix = " ")
-    if seqs.is_a?(Hash)
-      out_fasta_f = File.new(path, "w+")
-      seqs.each_key { |name|
-        out_fasta_f << ">#{prefix}#{name}" << $/ << seqs[name] << $/
-      }
-      out_fasta_f.close
-    else 
-      out_fasta_f = File.new(path, "w+")
-      seqs.each_with_index { |seq, i|
-        out_fasta_f << ">#{prefix}#{i+1}" << $/ << seq << $/
-      }
-      out_fasta_f.close
-    end
-  end
-  
-  def get_consensus(seqs)
-    report "consensus creating method should be checked, you are using unsafe code"
-    return 'nil' if seqs.size == 0
-    conslet = { 'A' => 'A', 'C' => 'C', 'G' => 'G', 'T' => 'T', 'U' => 'U',
-            'AG' => 'R', 'CT' => 'Y', 'GT' => 'K', 'AC' => 'M', 'CG' => 'S', 'AT' => 'W',
-            'CGT' => 'B', 'AGT' => 'D', 'ACT' => 'H', 'ACG' => 'V', 'ACGT' => 'N'
-    }
-    new_consensus, letters = '', []
-    0.upto(seqs[0].size-1) { |i|
-      seqs.each do |word|
-        letters << word[i] if !letters.include?(word[i])
-      end
-      letters.sort!
-      letters_string = ''
-      letters.each do |letter| letters_string << letter end
-      checkerr("cannot find consensus letter for a given letter set :#{}") { conslet[letters_string] == nil }
-      new_consensus << conslet[letters_string]	
-      letters.clear
-    }
-    return new_consensus
-  end
-
-  def Ytilib.new_mysql_conn(database)
-    my = Mysql.new(MYSQL_HOST, MYSQL_USER, MYSQL_PASSWORD, database)
-    checkerr("cannot connect to MySQL server") { my.query("select 1").fetch_row[0] != "1" }
-    return my
-  end  
-  
-
-end
-
-#report "ytilib required, working directory #{Dir.pwd}", "ytilib"
-include Ytilib