Top Level Namespace

Includes:
Ytilib

Defined Under Namespace

Modules: Magick, REXML, SequenceLogo, Ytilib Classes: Array, File, Float, IUPAC, Integer, Object, PPM, String

Constant Summary

Constants included from Ytilib

Ytilib::STRAND_DIRECT, Ytilib::STRAND_REVCOMP

Instance Method Summary collapse

Methods included from Ytilib

#get_consensus, mfa2array, new_mysql_conn, read_mfa2array, read_mfa2hash, read_plain2array, read_seqs2array, time, write_mfa

Instance Method Details

#arglist_augmented_with_stdin(argv) ⇒ Object 



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# File 'lib/sequence_logo/exec/sequence_logo.rb', line 19

def arglist_augmented_with_stdin(argv)
  result = argv
  result += $stdin.read.shellsplit  unless $stdin.tty?
  result
end

#checkerr(message = "checkerr failed") ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 21

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

#direct_output_filename(output_file) ⇒ Object 



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# File 'lib/sequence_logo/exec/glue_logos.rb', line 50

def direct_output_filename(output_file)
  extname = File.extname(output_file)
  basename = File.basename_wo_extname(output_file)
  dirname = File.dirname(output_file)
  File.join(dirname, "#{basename}_direct#{extname}")
end

#get_ppm_from_file(in_file_name) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ppm_support.rb', line 7

def get_ppm_from_file(in_file_name)
  case File.ext_wo_name(in_file_name)
  when 'pat', 'pcm'
    pm = PM.load(in_file_name)
    pm.fixwc  if pm.words_count
  when 'mfa', 'fasta', 'plain'
    pm = PM.new_pcm(Ytilib.read_seqs2array(in_file_name))
  when 'xml'
    pm = PM.from_bismark(Bismark.new(in_file_name).elements["//PPM"])
  when in_file_name
    pm = PPM.from_IUPAC(in_file_name.upcase)
  end
  pm.get_ppm
rescue
  nil
end

#in_necessary_orientations(objects_to_render, orientation, logo_folder) ⇒ Object

{renderable: , name: }

–> [{renderable: , filename: }]



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# File 'lib/sequence_logo/exec/sequence_logo.rb', line 5

def in_necessary_orientations(objects_to_render, orientation, logo_folder)
  objects_to_render.map do |infos|
    case orientation
    when :direct
      {renderable: infos[:renderable], filename: "#{infos[:name]}.png" }
    when :revcomp
      {renderable: infos[:renderable].revcomp, filename: "#{infos[:name]}.png" }
    when :both
      [ {renderable: infos[:renderable], filename: "#{infos[:name]}_direct.png" },
        {renderable: infos[:renderable].revcomp, filename: "#{infos[:name]}_revcomp.png" } ]
    end
  end.flatten
end

#load_alignment_infos(alignment_lines) ⇒ Object 



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# File 'lib/sequence_logo/exec/glue_logos.rb', line 5

def load_alignment_infos(alignment_lines)
  alignment_lines.map{|line|
    filename, shift, orientation, motif_name = line.strip.split("\t")
    motif_name ||= File.basename(filename, File.extname(filename))
    shift = shift.to_i
    orientation = orientation.downcase.to_sym

    ppm = get_ppm_from_file(filename)
    checkerr("bad input file: #{filename}") { ppm == nil }
    ppm.name ||= motif_name

    raise 'Unknown orientation'  unless [:direct, :revcomp].include?(orientation)

    ppm_oriented = (orientation == :direct) ? ppm : ppm.revcomp
    {motif: ppm_oriented, shift: shift}
  }
end

#make_logo_alignment(aligned_motifs, options) ⇒ Object 



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# File 'lib/sequence_logo/exec/glue_logos.rb', line 23

def make_logo_alignment(aligned_motifs, options)
  alignment = SequenceLogo::Alignment.new
  aligned_motifs.map {|motif_infos|
     = SequenceLogo::PPMLogo.new(motif_infos[:motif],
                                        icd_mode: options[:icd_mode],
                                        words_count: options[:words_count],
                                        enable_threshold_lines: options[:threshold_lines])
    alignment += SequenceLogo::Alignment::Item.new(, motif_infos[:shift])
  }
  alignment
end

#readlines_from_file_or_stdin(argv, options = {}) ⇒ Object 



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# File 'lib/sequence_logo/exec/glue_logos.rb', line 35

def readlines_from_file_or_stdin(argv, options = {})
  default_options = { source_not_given_msg: 'Specify input data',
                      both_sources_given_msg: 'Specify either file with data or data itself in stdin, not both'}
  options = default_options.merge(options)
  raise options[:both_sources_given_msg]  if !argv.empty? && !$stdin.tty?
  if !argv.empty?
    lines = File.readlines(argv.first)
  elsif !$stdin.tty?
    lines = $stdin.readlines
  else
    raise ArgumentError, options[:source_not_given_msg]
  end
  lines
end

#report(message, program_name = nil) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 15

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

#reverse_output_filename(output_file) ⇒ Object 



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# File 'lib/sequence_logo/exec/glue_logos.rb', line 57

def reverse_output_filename(output_file)
  extname = File.extname(output_file)
  basename = File.basename_wo_extname(output_file)
  dirname = File.dirname(output_file)
  File.join(dirname, "#{basename}_revcomp#{extname}")
end

#start(fullpath) ⇒ Object 



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# File 'lib/sequence_logo/ytilib/ytilib.rb', line 9

def start(fullpath)
  report(fullpath + ARGV.inject("") { |out, v| out += " " + v})
  return if $NO_REPORT
  $program_name = "[#{File.name_wo_ext(fullpath)}]"
end