Module: Qu::Cmdwrapper

Defined in:
lib/qu/cmdwrapper.rb,
lib/qu/cmdwrapper/cmd.rb,
lib/qu/cmdwrapper/version.rb

Defined Under Namespace

Classes: ShellError

Constant Summary collapse

BIN_ROOT = 
File.join(__dir__, 'ext_bin')
BIN_PATH = 
File.join(BIN_ROOT, Utils::platform_os, Utils::platform_bit.to_s)
THERMO_PATH = 
File.join(__dir__, 'primer3_config') + '/'
VERSION = 
"1.0.5"

Class Method Summary collapse

Class Method Details

.faToTwoBit(fasta, twobit) ⇒ Object 



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# File 'lib/qu/cmdwrapper/cmd.rb', line 101

def faToTwoBit(fasta, twobit)
  cmd = File.join(BIN_PATH, 'faToTwoBit')
  `#{cmd} #{fasta} #{twobit}`
end

.get_binding_seq_list(binding_range_list, twobit_file) ⇒ Object 



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# File 'lib/qu/cmdwrapper/cmd.rb', line 126

def get_binding_seq_list(binding_range_list, twobit_file) 
  amp_seq_list = []
  
  return amp_seq_list if binding_range_list.empty?

  begin
    fh = Tempfile.new('binding_range_list')
    fh.write(binding_range_list.join("\n"))
    fh.close
    amp_seq_list = twoBitToFa(fh.path, twobit_file)
  ensure
    fh.unlink
  end
  return amp_seq_list   
end

.ntthal(s1:, s2: nil, mv: 50, dv: 1.5, d: 50, n: 0.25, mode: 'ANY', tm_only: false) ⇒ Object 



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# File 'lib/qu/cmdwrapper/cmd.rb', line 31

def ntthal(s1:, s2: nil, mv: 50, dv: 1.5, d: 50, n: 0.25, mode: 'ANY', tm_only: false)
  cmd = File.join(BIN_PATH, 'ntthal')

  if s2
    # tm = `#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -s2 #{s2} -r -path #{THERMO_PATH} -a #{mode}`
    # out = `#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -s2 #{s2} -path #{THERMO_PATH} -a #{mode}`
    out = system_quietly("#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -s2 #{s2} -path #{THERMO_PATH} -a #{mode}")
  else
    # out = `#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -path #{THERMO_PATH} -a HAIRPIN`
    out = system_quietly("#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -path #{THERMO_PATH} -a HAIRPIN")
  end

  begin
    lines = out.lines

    tm = nil
    dg = nil
    if lines.shift =~ /.*dG\s+=\s+(-?\d+\.?\d+)\s+t\s+=\s+(\d+\.?\d+)/
      dg = $1.to_f / 1000
      tm = $2.to_f
    end

    if tm_only
      return tm
    end

    lines = lines.map {|line| line.split("\t")[1].chomp}

    if s2
      seq_1 = ''
      align = ''
      seq_2 = ''
      # puts lines
      (0...lines[0].size).each do |index|
        if lines[1][index] != ' '
          seq_1 << lines[1][index]
          seq_2 << lines[2][index]
          align << '|'
        else
          align << ' '
          seq_1 << lines[0][index]
          seq_2 << lines[3][index]
        end
      end

      seq_1.sub!(/\-+$/, '')
      return tm, dg, seq_1, align, seq_2

    else
      align = lines[0]
      seq = lines[1]

      return tm, dg, seq, align
    end

  rescue Exception => e

    if tm_only
      return 0
    else
      if s2
        return nil, nil, '', '', ''
      else
        return nil, nil, '', ''
      end
    end
  end

end

.primer3_core(p3_input_file) ⇒ Object 



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# File 'lib/qu/cmdwrapper/cmd.rb', line 17

def primer3_core(p3_input_file)
  begin
    cmd = File.join(BIN_PATH, 'primer3_core')
    begin
      return system_quietly("#{cmd} #{File.realpath(p3_input_file)}")
    rescue ShellError
      return ''
    end
  rescue IOError
    $stderr.puts "Primer3 input file not exists: #{p3_input_file}"
    exit
  end
end

.system_quietly(*cmd) ⇒ Object 



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# File 'lib/qu/cmdwrapper/cmd.rb', line 144

def system_quietly(*cmd)
  exit_status=nil
  err=nil
  out=nil
  Open3.popen3(*cmd) do |stdin, stdout, stderr, wait_thread|
    err = stderr.gets(nil)
    out = stdout.gets(nil)
    [stdin, stdout, stderr].each{|stream| stream.send('close')}
    exit_status = wait_thread.value
  end
  if exit_status.to_i > 0
    err = err.chomp if err
    raise ShellError, err
  elsif out
    return out.chomp
  else
    return true
  end
end

.twoBitToFa(seq_list_file, twobit_file) ⇒ Object 



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# File 'lib/qu/cmdwrapper/cmd.rb', line 106

def twoBitToFa(seq_list_file, twobit_file)
  cmd = File.join(BIN_PATH, 'twoBitToFa')

  records = []
  begin
    out_file = Tempfile.new('twobit')
    `#{cmd} -seqList=#{seq_list_file} #{twobit_file} #{out_file.path}`
    out_file.rewind

    Bio::FlatFile.new(Bio::FastaFormat, out_file).each do |record|
      records << record.naseq.seq
    end
  ensure
    out_file.close
    out_file.unlink
  end

  return records
end