Module: Ytilib

Includes:
REXML
Defined in:
lib/sequence_logo/ytilib/infocod.rb,
lib/sequence_logo/ytilib/pm.rb,
lib/sequence_logo/ytilib/pmsd.rb,
lib/sequence_logo/ytilib/ytilib.rb,
lib/sequence_logo/ytilib/ytilib.rb,
lib/sequence_logo/ytilib/bismark.rb,
lib/sequence_logo/ytilib/randoom.rb

Overview

class Integer

@@fact_hash = {}
def log_fact
  return 0.0 if self == 0
  return nil if self < 0
  if self <= 170
    @@fact_hash[self] = Math.log( lambda { |k| return k if self.times { |i| k *= i.next } }.call(1) )
  else
    return self.to_f.log_fact
  end unless @@fact_hash.has_key?(self)
  return @@fact_hash[self] 
end

end

Defined Under Namespace

Modules: Randoom Classes: Bismark, PM, PPM

Constant Summary collapse

STRAND_DIRECT = 
"direct"
STRAND_REVCOMP = 
"revcomp"

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.mfa2array(input) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 66

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

.new_mysql_conn(database) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 137

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

.read_mfa2array(path) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 50

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

.read_mfa2hash(path) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 33

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

.read_plain2array(path) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 79

def Ytilib.read_plain2array(path)
  array = []
  File.open(path).each_line { |line|
    array << line.strip if !line.strip.empty?
  }
  return array
end

.read_seqs2array(path) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 87

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

.time ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 2

def Ytilib.time
  return Time.now.strftime('%d %b %H:%M:%S')
end

.write_mfa(seqs, path, prefix = " ") ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 99

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

Instance Method Details

#get_consensus(seqs) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 115

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