Module: Iroki::CoreExt::File

Defined in:
lib/iroki/core_ext/file/file.rb

Instance Method Summary collapse

Instance Method Details

#check_file(arg, which) ⇒ Object 



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# File 'lib/iroki/core_ext/file/file.rb', line 51

def check_file arg, which
  help = " Try iroki --help for help."

  abort_if arg.nil?,
           "You must provide a #{which} file.#{help}"

  abort_unless Object::File.exists?(arg),
               "The file '#{arg}' doesn't exist.#{help}"

  arg
end

#parse_color_map(fname, exact_matching: true, auto_color: false) ⇒ Object

TODO this is now pointless



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# File 'lib/iroki/core_ext/file/file.rb', line 64

def parse_color_map fname,
                    exact_matching: true,
                    auto_color: false

  check_file fname, :color_map


  patterns = {}
  Object::File.open(fname, "rt").each_line do |line|
    unless line.start_with? "#"
      label_tag = ""
      branch_tag = ""

      pattern, label_color, branch_color = line.chomp.split "\t"

      # color = "black" if color.nil? || color.empty?

      assert pattern, "found no pattern"

      if exact_matching # TODO should this really be everytime?
        pattern = pattern#.clean_name
      else
        # TODO flag bad regexp
        pattern = Regexp.new pattern
      end

      if color_given?(label_color) && color_given?(branch_color)
        abort_if(has_label_tag?(label_color) &&
                 has_label_tag?(branch_color),
                 "Label tag specified twice for '#{line}'")

        abort_if(has_branch_tag?(label_color) &&
                 has_branch_tag?(branch_color),
                 "Branch tag specified twice for '#{line}'")
      end

      if color_given?(label_color) && !color_given?(branch_color)
        if (color = has_label_tag? label_color)
          label_tag = Iroki::Color.get_tag color, auto_color
        elsif (color = has_branch_tag? label_color)
          branch_tag = Iroki::Color.get_tag color, auto_color
        else
          label_tag = Iroki::Color.get_tag label_color, auto_color
          branch_tag = Iroki::Color.get_tag label_color, auto_color
        end
      else
        if color_given? label_color
          if (color = has_label_tag? label_color)
            label_tag = Iroki::Color.get_tag color, auto_color
          elsif (color = has_branch_tag? label_color)
            branch_tag = Iroki::Color.get_tag color, auto_color
          else
            label_tag = Iroki::Color.get_tag label_color, auto_color
          end
        end

        if color_given? branch_color
          if (color = has_branch_tag? branch_color)
            branch_tag = Iroki::Color.get_tag color, auto_color
          elsif (color = has_label_tag? branch_color)
            label_tag = Iroki::Color.get_tag color, auto_color
          else
            branch_tag = Iroki::Color.get_tag branch_color, auto_color
          end
        end
      end

      # if auto_color
      #   patterns[pattern] = "[&!color=\"#{auto_colors[color]}\"]"
      # else
      #   patterns[pattern] = Iroki::Color.get_tag color, auto_color
      # end

      patterns[pattern] = { label: label_tag, branch: branch_tag }
    end
  end

  patterns
end

#parse_color_map_iroki(fname, iroki_to_name, exact_matching: true, auto_color: false) ⇒ Object 



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# File 'lib/iroki/core_ext/file/file.rb', line 144

def parse_color_map_iroki(fname,
                          iroki_to_name,
                          exact_matching: true,
                          auto_color: false)


  check_file fname, :color_map

  name_to_iroki = iroki_to_name.invert

  patterns = {}
  Object::File.open(fname, "rt").each_line do |line|
    unless line.start_with? "#"
      label_tag = ""
      branch_tag = ""

      pattern, label_color, branch_color = line.chomp.split "\t"

      pattern.strip! if pattern
      label_color.strip! if label_color
      branch_color.strip! if branch_color

      # color = "black" if color.nil? || color.empty?

      assert pattern, "found no pattern"

      if exact_matching # TODO should this really be everytime?
      # pattern = pattern.clean_name
        if name_to_iroki.has_key? pattern
          pattern = name_to_iroki[pattern]
        else
          AbortIf::logger.info "String '#{pattern}' has no " +
                               "match in " +
                               "name_to_iroki map"
        end
      else
        # TODO flag bad regexp
        pattern = Regexp.new pattern
      end

      if color_given?(label_color) && color_given?(branch_color)
        abort_if(has_label_tag?(label_color) &&
                 has_label_tag?(branch_color),
                 "Label tag specified twice for '#{line}'")

        abort_if(has_branch_tag?(label_color) &&
                 has_branch_tag?(branch_color),
                 "Branch tag specified twice for '#{line}'")
      end

      if color_given?(label_color) && !color_given?(branch_color)
        if (color = has_label_tag? label_color)
          label_tag = Iroki::Color.get_tag color, auto_color
        elsif (color = has_branch_tag? label_color)
          branch_tag = Iroki::Color.get_tag color, auto_color
        elsif line.match(/\t\Z/) # empty branch color, branch will be black
          label_tag = Iroki::Color.get_tag label_color, auto_color
        else
          label_tag = Iroki::Color.get_tag label_color, auto_color
          branch_tag = Iroki::Color.get_tag label_color, auto_color
        end
      else
        if color_given? label_color
          if (color = has_label_tag? label_color)
            label_tag = Iroki::Color.get_tag color, auto_color
          elsif (color = has_branch_tag? label_color)
            branch_tag = Iroki::Color.get_tag color, auto_color
          else
            label_tag = Iroki::Color.get_tag label_color, auto_color
          end
        end

        if color_given? branch_color
          if (color = has_branch_tag? branch_color)
            branch_tag = Iroki::Color.get_tag color, auto_color
          elsif (color = has_label_tag? branch_color)
            label_tag = Iroki::Color.get_tag color, auto_color
          else
            branch_tag = Iroki::Color.get_tag branch_color, auto_color
          end
        end
      end

      # if auto_color
      #   patterns[pattern] = "[&!color=\"#{auto_colors[color]}\"]"
      # else
      #   patterns[pattern] = Iroki::Color.get_tag color, auto_color
      # end

      patterns[pattern] = { label: label_tag, branch: branch_tag }
    end
  end

  patterns
end

#parse_name_map(fname) ⇒ Object 



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# File 'lib/iroki/core_ext/file/file.rb', line 241

def parse_name_map fname
  check_file fname, :name_map

  name_map = {}
  Object::File.open(fname, "rt").each_line do |line|
    unless line.start_with? "#"
      abort_if line.chomp.split("\t").count > 2,
               "Line (#{line.inspect}) has more than two columns"

      oldname, newname = line.chomp.split "\t"

      oldname.strip! if oldname
      newname.strip! if newname

      abort_if oldname.nil? || oldname.empty?,
               "Column 1 missing for line: #{line.inspect}"

      abort_if newname.nil? || newname.empty?,
               "Column 2 missing for line: #{line.inspect}"

      # oldname = oldname.clean_name
      # newname = newname.clean_name

      abort_if name_map.has_key?(oldname),
               "#{oldname} is repeated in column 1"

      name_map[oldname] = newname
    end
  end

  abort_if duplicate_values?(name_map),
           "Names in column 2 of name map file must be unique"

  name_map
end

#valid_newick?(fname) ⇒ Boolean

Note:

Only checks that first and last chars off the file (minus trailing newlines) are correct. I.e., first char is ‘(’ and last char is ‘;’

Returns:

  • (Boolean) 


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# File 'lib/iroki/core_ext/file/file.rb', line 43

def valid_newick? fname
  str = Object::File.read(fname).chomp
  first_char = str[0]
  last_char = str[-1]

  first_char == "(" && last_char == ";"
end